public void getDriftProfileFromRawDataMZ_771_Test1() { Run run = TestUtilities.GetStandardUIMFRun(); UIMFRun uimfRun = (UIMFRun)run; DriftTimeProfileExtractor profileExtractor = new DriftTimeProfileExtractor(); FrameSet frameset = new FrameSet(805, 804, 806); double targetMZ1 = 746.3842; double targetMZ2 = 771.6894; ScanSetCollectionCreator ssc = new ScanSetCollectionCreator(run, 200, 350, 1, 1); ssc.Create(); System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch(); sw.Start(); XYData xydata = profileExtractor.ExtractProfileFromRawData(uimfRun, frameset, run.ScanSetCollection, targetMZ2, 10d); sw.Stop(); TestUtilities.DisplayXYValues(xydata); Console.WriteLine(sw.ElapsedMilliseconds); }
public void getDriftProfileFromRawDataMZ_967_Test1() { Run run = TestUtilities.GetStandardUIMFRun(); UIMFRun uimfRun = (UIMFRun)run; DriftTimeProfileExtractor profileExtractor = new DriftTimeProfileExtractor(); FrameSet frameset = new FrameSet(804, 803, 805); uimfRun.CurrentFrameSet = frameset; double targetMZ = 967.26; ScanSetCollectionCreator ssc = new ScanSetCollectionCreator(run, 200, 350, 9, 1); ssc.Create(); //XYData xydata = profileExtractor.ExtractProfileFromRawData(uimfRun, frameset, run.ScanSetCollection, targetMZ, 30d); createPeaks(run); XYData xydata = profileExtractor.ExtractProfileFromPeakData(uimfRun, frameset, run.ScanSetCollection, targetMZ, 30d); TestUtilities.DisplayXYValues(xydata); }
public void exportAllPeaksInXCaliburFile() { if (File.Exists(xcaliburAllPeaksFileName)) { File.Delete(xcaliburAllPeaksFileName); } Run run = new XCaliburRun(xcaliburTestfile); ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false); scansetCreator.Create(); Task msgen = new GenericMSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task peakDetector = new DeconToolsPeakDetector(peakParams); ((DeconToolsPeakDetector)peakDetector).StorePeakData = true; Task exporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListTextExporter(run.MSFileType, 1000000, xcaliburAllPeaksFileName); //trigger of 1E5 = 310 sec (memory = 150 MB); trigger of 1E6 = 231 Sec (memory = 250 MB); foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); exporter.Execute(run.ResultCollection); } exporter.Cleanup(); Assert.AreEqual(true, File.Exists(xcaliburAllPeaksFileName)); }
public void criticalErrorInPeakDetectorTest1() { UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2); FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 425, 432, 3, 1); ffcc.Create(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 500, 9, 1); sscc.Create(); MSGeneratorFactory factory = new MSGeneratorFactory(); Task msgen = factory.CreateMSGenerator(run.MSFileType); DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(); peakDet.PeakBackgroundRatio = 4; peakDet.SigNoiseThreshold = 3; foreach (var frame in run.FrameSetCollection.FrameSetList) { run.CurrentFrameSet = frame; foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); } } }
public void outputToSqlite_uimf_test1() { List <Run> runcoll = new List <Run>(); Run run = new UIMFRun(uimfFile1); runcoll.Add(run); FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 809, 3, 1); fsc.Create(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 220, 9, 1); sscc.Create(); Task msgen = new UIMF_MSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new RapidDeconvolutor(); Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor(); Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor(); Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor(); Task scanResultUpdater = new ScanResultUpdater(); Task sqliteExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.UIMFScanResult_SqliteExporter(uimf_Sqlite_ScanResultOutputFile1); Stopwatch sw; foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList) { ((UIMFRun)run).CurrentFrameSet = frame; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); ticExtractor.Execute(run.ResultCollection); scanResultUpdater.Execute(run.ResultCollection); driftTimeExtractor.Execute(run.ResultCollection); origIntensExtr.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); sqliteExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds); } } } }
public void weirdZeroValuesForMZsAtEarlyFramesTest1() { UIMFRun run = new UIMFRun(uimfTestfile1); FrameSetCollectionCreator framecreator = new FrameSetCollectionCreator(run, 1, 10, 5, 1); framecreator.Create(); ScanSetCollectionCreator scanCreator = new ScanSetCollectionCreator(run, 1, 1); scanCreator.Create(); Task msgen = new UIMF_MSGenerator(0, 5000); Task peakDet = new DeconToolsPeakDetector(); int scanstop = 599; int scanstart = 0; for (int i = scanstart; i < scanstop; i++) { run.CurrentFrameSet = run.FrameSetCollection.GetFrameSet(1); run.CurrentScanSet = run.ScanSetCollection.GetScanSet(i); msgen.Execute(run.ResultCollection); if (run.XYData != null && run.XYData.Xvalues != null && run.XYData.Xvalues[0] == 0) { reportXYValues(run); } } }
public void getDriftProfileMZ_796_Test1() //** { Run run = TestUtilities.GetStandardUIMFRun(); UIMFRun uimfRun = (UIMFRun)run; DriftTimeProfileExtractor profileExtractor = new DriftTimeProfileExtractor(); FrameSet frameset = new FrameSet(616, 615, 617); uimfRun.CurrentFrameSet = frameset; double targetMZ = 1004.1987; ScanSetCollectionCreator ssc = new ScanSetCollectionCreator(run, 200, 350, 1, 1); ssc.Create(); XYData xydata = profileExtractor.ExtractProfileFromRawData(uimfRun, frameset, run.ScanSetCollection, targetMZ, 30d); TestUtilities.DisplayXYValues(xydata); Console.WriteLine("-------------------------------------------------------------------------------------"); createPeaks(run); xydata = profileExtractor.ExtractProfileFromPeakData(uimfRun, frameset, run.ScanSetCollection, targetMZ, 30d); TestUtilities.DisplayXYValues(xydata); }
public void turnRAPIDScoreIntoHornScoreAndCompareTest1() { Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050); int numScansSummed = 1; ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, numScansSummed, 1, false); scanSetCreator.Create(); Task msgen = new GenericMSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters detParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detParams.PeakBackgroundRatio = 3; detParams.SignalToNoiseThreshold = 3; Task peakDet = new DeconToolsPeakDetector(detParams); Task rapid = new RapidDeconvolutor(); Task horn = new HornDeconvolutor(); Task fitcalc = new DeconToolsFitScoreCalculator(); run.CurrentScanSet = run.ScanSetCollection.GetScanSet(6005); msgen.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); horn.Execute(run.ResultCollection); //string isosData = reportIsotopicProfiles(run); //Console.Write(isosData); //First evaluate HornTransform score Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.GetMZ()); Assert.AreEqual(0.0101245114907111, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score); run.ResultCollection.ClearAllResults(); horn.Execute(run.ResultCollection); fitcalc.Execute(run.ResultCollection); Assert.AreEqual(0.00583991502104572, (decimal)run.ResultCollection.ResultList[0].IsotopicProfile.Score); run.ResultCollection.ClearAllResults(); //Run RAPID and evaluate the score Rapid gives it rapid.Execute(run.ResultCollection); Assert.AreEqual(481.274105402604, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.GetMZ()); Assert.AreEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score); //Run the DeconToolsFitScoreCalculator fitcalc.Execute(run.ResultCollection); //Evaluate the score given by the fitscore calculator Assert.AreNotEqual(1.52062147024669, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score); Assert.AreEqual(0.00583991502104572m, (decimal)run.ResultCollection.ResultList[7].IsotopicProfile.Score); }
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 uimfTest2() //ScanSets are created based on the number of scans per frame { Run run = new UIMFRun(uimfFilepath); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 700, 800, 3, 1, false); creator.Create(); }
public void simpleAddTest1() { //first deconvolute with THRASH //then deconvolute with RAPID, using comboMode = 'simplyAddIt' //so there will be duplicate results Project.Reset(); Run run = new XCaliburRun(xcaliburTestfile, 6000, 6050); Project.getInstance().RunCollection.Add(run); ResultCollection results = new ResultCollection(run); TaskCollection taskCollection = new TaskCollection(); ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false); scansetCreator.Create(); Task msgen = new GenericMSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters peakDetParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); peakDetParams.SignalToNoiseThreshold = 3; peakDetParams.PeakBackgroundRatio = 0.5; Task peakDetector = new DeconToolsPeakDetector(peakDetParams); Task thrashDecon = new HornDeconvolutor(); Task rapidDecon = new RapidDeconvolutor(); taskCollection.TaskList.Add(msgen); taskCollection.TaskList.Add(peakDetector); taskCollection.TaskList.Add(thrashDecon); TaskController taskcontroller = new BasicTaskController(taskCollection); taskcontroller.Execute(Project.getInstance().RunCollection); Assert.AreEqual(644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count); taskCollection.TaskList.Remove(thrashDecon); taskCollection.TaskList.Add(rapidDecon); Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear(); taskcontroller.Execute(Project.getInstance().RunCollection); Assert.AreEqual(2472, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count); Project.getInstance().RunCollection[0].ResultCollection.ResultList.Clear(); taskCollection.TaskList.Remove(rapidDecon); taskCollection.TaskList.Add(thrashDecon); taskCollection.TaskList.Add(rapidDecon); taskcontroller.Execute(Project.getInstance().RunCollection); Assert.AreEqual(2472 + 644, Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count); }
public void uimf_data_preLoaded() // in this case, data is preloaded, preventing re-accessing the same drifttimes over and over { Run run = new UIMFRun(uimfFilepath); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1); fscc.Create(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1); sscc.Create(); ((UIMFRun)run).GetFrameDataAllFrameSets(); // this is the key line... loads data necessary for drift time calc and correction UIMF_MSGenerator msgen = new UIMF_MSGenerator(); DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(); peakDet.PeakBackgroundRatio = 6; peakDet.SigNoiseThreshold = 3; HornDeconvolutor decon = new HornDeconvolutor(); UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor(); StringBuilder sb = new StringBuilder(); foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList) { ((UIMFRun)run).CurrentFrameSet = frame; foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); driftTimeExtractor.Execute(run.ResultCollection); } } foreach (var item in run.ResultCollection.ResultList) { UIMFIsosResult isosresult = (UIMFIsosResult)item; sb.Append(isosresult.FrameSet.PrimaryFrame); sb.Append("\t"); sb.Append(isosresult.ScanSet.PrimaryScanNumber); sb.Append("\t"); sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000")); sb.Append("\t"); sb.Append(isosresult.DriftTime.ToString("0.000")); sb.Append(Environment.NewLine); } Console.Write(sb.ToString()); }
public void checkIntegrityOfUIMF_RawDataTest1() { UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2); FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 696, 696, 3, 1); ffcc.Create(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 350, 500, 9, 1); sscc.Create(); MSGeneratorFactory factory = new MSGeneratorFactory(); Task msgen = factory.CreateMSGenerator(run.MSFileType); DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(); peakDet.PeakBackgroundRatio = 6; peakDet.SigNoiseThreshold = 3; StringBuilder sb = new StringBuilder(); sb.Append("frame\tscan\tmaxIntens\tnumZeros\n"); foreach (var frame in run.FrameSetCollection.FrameSetList) { run.CurrentFrameSet = frame; foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); List <int> indices = getIndicesOf0MZValues(run.XYData.Xvalues); double maxY = run.XYData.GetMaxY(); if (indices.Count > -1) { sb.Append(frame.PrimaryFrame); sb.Append("\t"); sb.Append(scan.PrimaryScanNumber); sb.Append("\t"); sb.Append(maxY); sb.Append("\t"); sb.Append(indices.Count); sb.Append("\n"); } } } Console.WriteLine(sb.ToString()); }
public void xcaliburSpeed_RAPID_Test1() { Run run = new XCaliburRun(xcaliburTestfile); int startScan = 6005; int stopScan = 7000; 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(); Task rapid = new RapidDeconvolutor(); rapid.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); }
public void uimf_data_not_preLoaded() // in this case the drift time is calculated every time by looking up sqlite data from uimf file { Run run = new UIMFRun(uimfFilepath); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1); fscc.Create(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1); sscc.Create(); UIMF_MSGenerator msgen = new UIMF_MSGenerator(); DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(); peakDet.PeakBackgroundRatio = 6; peakDet.SigNoiseThreshold = 3; HornDeconvolutor decon = new HornDeconvolutor(); UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor(); StringBuilder sb = new StringBuilder(); foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList) { ((UIMFRun)run).CurrentFrameSet = frame; foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); driftTimeExtractor.Execute(run.ResultCollection); } } foreach (var item in run.ResultCollection.ResultList) { UIMFIsosResult isosresult = (UIMFIsosResult)item; sb.Append(isosresult.FrameSet.PrimaryFrame); sb.Append("\t"); sb.Append(isosresult.ScanSet.PrimaryScanNumber); sb.Append("\t"); sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000")); sb.Append("\t"); sb.Append(isosresult.DriftTime.ToString("0.000")); sb.Append(Environment.NewLine); } Console.Write(sb.ToString()); }
public void uimfTest1() //ScanSets are created based on the number of scans per frame { Run run = new UIMFRun(uimfFilepath); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 3, 1); creator.Create(); Assert.AreEqual(600, run.ScanSetCollection.ScanSetList.Count); }
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 basicCreatorTestWithAlternateConstructorTest4() { Run run = new XCaliburRun(xcaliburTestfile); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 1, 19000, 1, 1, false); //get all MS-Level scans creator.Create(); Assert.AreEqual(2695, run.ScanSetCollection.ScanSetList.Count); Assert.AreEqual(new int[] { 1 }, run.ScanSetCollection.ScanSetList[0].IndexValues.ToArray()); }
public void basicCreatorTestWithAlternateConstructorTest2() { Run run = new XCaliburRun(xcaliburTestfile); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 6000, 7000, 1, 1, false); creator.Create(); Assert.AreEqual(145, run.ScanSetCollection.ScanSetList.Count); Assert.AreEqual(new int[] { 6005 }, run.ScanSetCollection.ScanSetList[0].IndexValues.ToArray()); //first scan is 6005, a MS-level scan }
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 outputToText_xcaliburData_Test1() { string testFile = xcalibur_text_IsosResultOutputFile1; List <Run> runcoll = new List <Run>(); Run run = new XCaliburRun(xcaliburFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false); sscc.Create(); Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new HornDeconvolutor(); Task flagger = new ResultValidatorTask(); Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.BasicIsosResultTextFileExporter(testFile); Task peakExporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListSQLiteExporter(100000, peakExporter1); Stopwatch sw; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); isosExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("Exporter execution time = \t" + sw.ElapsedMilliseconds); } peakExporter.Execute(run.ResultCollection); } Assert.AreEqual(true, File.Exists(testFile)); FileInfo fi = new FileInfo(testFile); //Assert.AreEqual(25881, fi.Length); Console.Write(fi.Length); }
public void basicCreatorTest1() { Run run = new XCaliburRun(xcaliburTestfile); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 3, 1); creator.Create(); Assert.AreEqual(2695, run.ScanSetCollection.ScanSetList.Count); TestUtilities.DisplayScanSetData(run.ScanSetCollection.ScanSetList); //Assert.AreEqual(new int[] { 0, 1, 2 }, run.ScanSetCollection.ScanSetList[0].IndexValues.ToArray()); //Assert.AreEqual(new int[] { 18504, 18505 }, run.ScanSetCollection.ScanSetList[18504].IndexValues.ToArray()); }
public void outputToText_xcaliburData_Test1() { List <Run> runcoll = new List <Run>(); Run run = new XCaliburRun(xcaliburFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6100, 1, 1); sscc.Create(); Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new RapidDeconvolutor(); Task textScanResultExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.BasicScanResult_TextFileExporter(xcalibur_text_ScanResultOutputFile1); Task scanResultUpdater = new ScanResultUpdater(); Stopwatch sw; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); scanResultUpdater.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); textScanResultExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("Exporter execution time = \t" + sw.ElapsedMilliseconds); } } //TaskCollection taskColl=new TaskCollection(); //taskColl.TaskList.Add(msgen); //taskColl.TaskList.Add(peakDetector); //taskColl.TaskList.Add(decon); //taskColl.TaskList.Add(sqliteExporter); //TaskController controller = new BasicTaskController(taskColl); //controller.Execute(runcoll); }
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 void xcaliburFile100ScanRAPIDTest1() { Project.Reset(); Run run = new XCaliburRun(xcaliburTestfile, 6000, 6999); Project project = Project.getInstance(); 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); Task rapidDecon = new RapidDeconvolutor(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(rapidDecon); 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(1000, project.RunCollection[0].ScanSetCollection.ScanSetList.Count); Assert.AreEqual(12762, 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 basicCreatorTestWithAlternateConstructor_MSMSIncludedTest1() { Run run = new XCaliburRun(xcaliburTestfile); ScanSetCollectionCreator creator = new ScanSetCollectionCreator(run, 6000, 7000, 3, 1, true); System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch(); sw.Start(); creator.Create(); sw.Stop(); Console.WriteLine(sw.ElapsedMilliseconds); //Assert.AreEqual(1001, run.ScanSetCollection.ScanSetList.Count); Assert.AreEqual(new int[] { 5999, 6000, 6001 }, run.ScanSetCollection.ScanSetList[0].IndexValues.ToArray()); }
public void test1() { Run run0 = new XCaliburRun(c2_blankfilePath); Run run1 = new XCaliburRun(c2_6FilePath); Run run2 = new XCaliburRun(c2_7FilePath); Run run3 = new XCaliburRun(c2_8FilePath); Run run4 = new XCaliburRun(c2_9FilePath); Run run5 = new XCaliburRun(c2_10FilePath); Project.getInstance().RunCollection.Add(run0); Project.getInstance().RunCollection.Add(run1); Project.getInstance().RunCollection.Add(run2); Project.getInstance().RunCollection.Add(run3); Project.getInstance().RunCollection.Add(run4); Project.getInstance().RunCollection.Add(run5); foreach (Run run in Project.getInstance().RunCollection) { ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, 1, 1); scansetCreator.Create(); } Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new SimpleDecon(); Task isosMergerExporter = new BasicIsosMergerExporter("..\\..\\TestFiles\\MergeTestFiles\\BasicIsosMergerExporterTest1Output_isos.csv"); Task scansupdater = new ScanResultUpdater(); Task scansMergerExporter = new BasicScansMergerExporter("..\\..\\TestFiles\\MergeTestFiles\\BasicIsosMergerExporterTest1Output_scans.csv"); Project.getInstance().TaskCollection.TaskList.Add(msgen); Project.getInstance().TaskCollection.TaskList.Add(peakDetector); Project.getInstance().TaskCollection.TaskList.Add(decon); Project.getInstance().TaskCollection.TaskList.Add(isosMergerExporter); Project.getInstance().TaskCollection.TaskList.Add(scansupdater); Project.getInstance().TaskCollection.TaskList.Add(scansMergerExporter); BasicTaskController taskController = new BasicTaskController(Project.getInstance().TaskCollection); taskController.Execute(Project.getInstance().RunCollection); TaskCleaner cleaner = new TaskCleaner(Project.getInstance().TaskCollection); cleaner.CleanTasks(); }
public void examineEffectOfIntensityCutoffOnRapidTest1() { Project project = Project.getInstance(); project.Parameters.OldDecon2LSParameters = new OldDecon2LSParameters(); Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000); project.RunCollection.Add(run); ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1); scansetCreator.Create(); ResultCollection results = new ResultCollection(run); foreach (ScanSet scanset in run.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); for (int i = 1; i < 6; i++) { results.ResultList.Clear(); Task rapidDecon = new RapidDeconvolutor(i, DeconTools.Backend.ProcessingTasks.IDeconvolutor.DeconResultComboMode.simplyAddIt); rapidDecon.Execute(results); //Console.WriteLine(scanset.PrimaryScanNumber + "\t" + i + "\t" + // results.ResultList.Count + "\t" + results.Run.CurrentScanSet.BackgroundIntensity); } } }
public void examineFPGAFileTest1() { UIMFRun run = new UIMFRun(uimfFPGAFilePath); 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(); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 300, 300, 1, 1); sscc.Create(); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 5, 5, 1, 1); fscc.Create(); foreach (var frame in run.FrameSetCollection.FrameSetList) { run.CurrentFrameSet = frame; foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msGen.Execute(run.ResultCollection); //TestUtilities.DisplayXYValues(run.XYData); originalIntensitiesExtractor.Execute(run.ResultCollection); TestUtilities.DisplayXYValues(run.XYData); } } }
public void outputToSqlite_xcaliburData_Test1() { List <Run> runcoll = new List <Run>(); Run run = new XCaliburRun(xcaliburFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6100, 1, 1, false); sscc.Create(); Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new RapidDeconvolutor(); Task sqliteScanResultExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.BasicScanResult_SqliteExporter(xcalibur_sqlite_ScanResultOutputFile1); Task peakExporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListSQLiteExporter(100000, peakExporter1); Task scanResultUpdater = new ScanResultUpdater(); Stopwatch sw; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); scanResultUpdater.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); sqliteScanResultExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds); } peakExporter.Execute(run.ResultCollection); } }