public void serializeUIMFDataTest1() { Run run = new UIMFRun(uimfFilepath2); List <Run> runCollection = new List <Run>(); runCollection.Add(run); int startFrame = 1200; int stopFrame = 1205; int numFramesSummed = 3; int numScansSummed = 3; FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1); framesetCreator.Create(); ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1); scanSetCreator.Create(); Task msgen = new UIMF_MSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 3; detectorParams.ThresholdedData = true; Task peakdetector = new DeconToolsPeakDetector(detectorParams); Task decon = new RapidDeconvolutor(); TaskCollection taskcollection = new TaskCollection(); taskcollection.TaskList.Add(msgen); taskcollection.TaskList.Add(peakdetector); taskcollection.TaskList.Add(decon); TaskController taskcontroller = new UIMF_TaskController(taskcollection); taskcontroller.IsosResultThresholdNum = 50; taskcontroller.Execute(runCollection); ResultCollection results; IsosResultDeSerializer deserializer = new IsosResultDeSerializer(run.Filename + "_tmp.bin"); int counter = 0; do { counter++; results = deserializer.GetNextSetOfResults(); } while (results != null); Assert.AreEqual(8, counter); }
public void test1_summing() { Project.Reset(); Project project = Project.getInstance(); UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1201); project.RunCollection.Add(run); int numFramesSummed = 3; int numScansSummed = 3; ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, numScansSummed, 1); sscc.Create(); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, numFramesSummed, 1); fscc.Create(); Task msGen = new UIMF_MSGenerator(200, 2000); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 3; Task peakDetector = new DeconToolsPeakDetector(detectorParams); Task decon = new HornDeconvolutor(); Task scanResultsUpdater = new ScanResultUpdater(); Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(decon); project.TaskCollection.TaskList.Add(scanResultsUpdater); project.TaskCollection.TaskList.Add(originalIntensitiesExtractor); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); ResultCollection rc = project.RunCollection[0].ResultCollection; Assert.AreEqual(180, rc.ResultList.Count); StringBuilder sb = new StringBuilder(); IsosResultUtilities.DisplayResults(sb, rc.ResultList); Console.Write(sb.ToString()); }
public void multipleFrames_horn_test1() { Project.Reset(); Project project = Project.getInstance(); project.LoadOldDecon2LSParameters(uimfParameters1); UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1203); project.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); Task peakDetector = new DeconToolsPeakDetector(project.Parameters.OldDecon2LSParameters.PeakProcessorParameters); Task decon = new HornDeconvolutor(project.Parameters.OldDecon2LSParameters.HornTransformParameters); Task scanResultsUpdater = new ScanResultUpdater(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(zeroFiller); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(decon); project.TaskCollection.TaskList.Add(scanResultsUpdater); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); sw.Stop(); 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); Console.WriteLine("Peaks found = " + project.RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks); StringBuilder sb = new StringBuilder(); }
public void test1() { Project project = Project.getInstance(); //TODO: add project parameters (for summing) Run run = new UIMFRun(uimfFilepath, 1200, 1202, 300, 400); project.RunCollection.Add(run); FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, ((UIMFRun)run).MinFrame, ((UIMFRun)run).MaxFrame, 1, 1); framesetCreator.Create(); ScanSetCollectionCreator scanSetcreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false); scanSetcreator.Create(); Task msGen = new UIMF_MSGenerator(200, 2000); 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(); Task scanresultUpdater = new ScanResultUpdater(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(rapidDecon); project.TaskCollection.TaskList.Add(scanresultUpdater); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); UIMFScansExporter scansExporter = new UIMFScansExporter(uimfScansExporterTest1output); scansExporter.Export(project.RunCollection[0].ResultCollection); }
public void smallExportTest1() { Project project = Project.getInstance(); //TODO: add project parameters (for summing) project.RunCollection.Add(new UIMFRun(uimfFilepath, 1200, 1202, 250, 300)); Task msGen = new UIMF_MSGenerator(200, 2000); 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 decon = new HornDeconvolutor(); Task driftTimeExtractor = new UIMFDriftTimeExtractor(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(decon); project.TaskCollection.TaskList.Add(driftTimeExtractor); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); UIMFIsosExporter isosExporter = new UIMFIsosExporter(uimfIsosExporterTest1output); isosExporter.Export(project.RunCollection[0].ResultCollection); }
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 test1() { Project.Reset(); Project project = Project.getInstance(); UIMFRun run = new UIMFRun(uimfFilepath, 1200, 1202); project.RunCollection.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 1); sscc.Create(); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1); fscc.Create(); Task msGen = new UIMF_MSGenerator(200, 2000); 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(); Task scanResultsUpdater = new ScanResultUpdater(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(rapidDecon); project.TaskCollection.TaskList.Add(scanResultsUpdater); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); sw.Stop(); 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); Assert.AreEqual(1, Project.getInstance().RunCollection.Count); Assert.AreEqual(4, project.TaskCollection.TaskList.Count); Assert.AreEqual(600, project.RunCollection[0].ScanSetCollection.ScanSetList.Count); UIMFRun uimfRun = (UIMFRun)(project.RunCollection[0]); Assert.AreEqual(3, uimfRun.FrameSetCollection.FrameSetList.Count); StringBuilder sb = new StringBuilder(); foreach (IsosResult result in project.RunCollection[0].ResultCollection.ResultList) { Assert.IsInstanceOfType(typeof(UIMFIsosResult), result); UIMFIsosResult uimfResult = (UIMFIsosResult)result; sb.Append(uimfResult.FrameSet.PrimaryFrame); sb.Append("\t"); sb.Append(uimfResult.ScanSet.PrimaryScanNumber); sb.Append("\t"); sb.Append(uimfResult.IsotopicProfile.Peaklist[0].XValue); sb.Append("\t"); sb.Append(uimfResult.IsotopicProfile.GetAbundance()); sb.Append("\t"); //sb.Append(uimfResult.IsotopicProfile. sb.Append(Environment.NewLine); } Console.Write(sb.ToString()); }
public void test1() { Run uimfrun = new UIMFRun(inputUIMFFile1); int startFrame = 800; int stopFrame = 800; int numFramesSummed = 3; int numScansSummed = 9; FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(uimfrun, startFrame, stopFrame, numFramesSummed, 1); framesetCreator.Create(); ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(uimfrun, 230, 240, numScansSummed, 1, false); scansetCreator.Create(); Project project = Project.getInstance(); project.RunCollection.Add(uimfrun); Task msGen = new UIMF_MSGenerator(200, 2000); 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 decon = new HornDeconvolutor(); Task driftTimeExtractor = new UIMFDriftTimeExtractor(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(decon); project.TaskCollection.TaskList.Add(driftTimeExtractor); TaskController controller = new UIMF_TaskController(project.TaskCollection); controller.Execute(project.RunCollection); Assert.AreEqual(252, project.RunCollection[0].ResultCollection.ResultList.Count); if (File.Exists(outputFile1)) { File.Delete(outputFile1); } Stopwatch sw = new Stopwatch(); sw.Start(); UIMFSQLiteIsosExporter isosExporter = new UIMFSQLiteIsosExporter(outputFile1); isosExporter.Export(project.RunCollection[0].ResultCollection); sw.Stop(); Console.Write("\n\n----------- Time taken for UIMFSQLiteIsosExporter (milliseconds) = \t" + sw.ElapsedMilliseconds); }