public void findMSFeaturesInOrbitrapData_Test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
//order and get the most intense msfeature
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
var testIso = run.ResultCollection.ResultList[0];
Assert.AreEqual(13084442, testIso.IntensityAggregate);
Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
Assert.AreEqual(0.01012m, (decimal)Math.Round(testIso.IsotopicProfile.Score, 5));
Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
// TestUtilities.DisplayPeaks(run.PeakList);
}
public void effectOfFWHMOnFitTest()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1160, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[0];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var sb = new StringBuilder();
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
for (var fwhm = 0.001; fwhm < 0.050; fwhm = fwhm + 0.0005)
{
distcreator = new MercuryDistributionCreator();
resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / fwhm;
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
areafitter = new AreaFitter();
fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
}
//Console.Write(sb.ToString());
}
public void deconWithTHRASH_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
var validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0532199478712594m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void deconWithRAPID_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanSet scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
RapidDeconvolutor decon = new RapidDeconvolutor();
ResultValidatorTask validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(190, run.ResultCollection.ResultList.Count);
IsosResult testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0213668719893332m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void OldDeconvolutorTest_temp1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
#if !Disable_DeconToolsV2
var parameters = new DeconEngineClasses.OldDecon2LSParameters();
var paramFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_MaxFit1.xml";
parameters.Load(paramFile);
var scanSet = new ScanSetFactory().CreateScanSet(run, 6005, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var deconvolutor = new HornDeconvolutor(parameters.GetDeconToolsParameters());
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
deconvolutor.Execute(run.ResultCollection);
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//IsosResult testIso = run.ResultCollection.ResultList[0];
//TestUtilities.DisplayIsotopicProfileData(testIso.IsotopicProfile);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
#endif
}
public void getMSMSDataTest1()
{
//Create the run
var runFactory = new RunFactory();
var run = runFactory.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
//Create the task
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakdetector = new DeconToolsPeakDetectorV2();
var startScan = 6000;
var stopScan = 7000;
for (var i = startScan; i < stopScan; i++)
{
if (run.GetMSLevel(i) == 2)
{
var scanset = new ScanSet(i);
run.CurrentScanSet = scanset;
msgen.Execute(run.ResultCollection);
peakdetector.Execute(run.ResultCollection);
Console.Write("Working on Scan " + scanset.PrimaryScanNumber);
Console.WriteLine("; XYPair count = " + run.XYData.Xvalues.Length);
Console.WriteLine("num peaks= " + run.PeakList.Count);
}
}
}
public void PeakDetectorDemo1()
{
//In this list on Scan 6005 we can see what the peak of the parent is. Slide 4 1059.45898 is the Monoisotopic peak of Scan 6009
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var testScan = new ScanSet(6009);
run.CurrentScanSet = testScan;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var sb = new StringBuilder();
foreach (var peak in run.PeakList)
{
sb.Append(peak.XValue + "\t" + peak.Height + "\t" + peak.Width + "\n");
}
Console.WriteLine("----------------------PeakList---------------");
Console.WriteLine("m/z\tintensity\twidth");
Console.WriteLine(sb.ToString());
}
public void peak_interference_UIMF_expectInterference_test1()
{
var uimfFrame1200_142 = FileRefs.RawDataBasePath + @"\UIMF\Sarc_MS_90_21Aug10_Cheetah_10-08-02_0000_frame1200_scan142.txt";
Run run = new DeconTools.Backend.Runs.MSScanFromTextFileRun(uimfFrame1200_142);
var scanSet = new ScanSet(0);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
msgen.MinMZ = 200;
msgen.MaxMZ = 2000;
var peakDetector = new DeconToolsPeakDetectorV2(4, 3, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
decon.MinIntensityForScore = 10;
decon.DeleteIntensityThreshold = 10;
decon.MaxFitAllowed = 0.4;
decon.MinMZ = 200;
decon.MaxMZ = 2000;
decon.IsMZRangeUsed = false;
var zeroFiller = new DeconToolsZeroFiller();
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 428 && p.IsotopicProfile.MonoPeakMZ < 430).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public void PeakDetectorOnCentroidedDataTest1()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6006); //this is a centroided MS2 scan
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true);
peakDetector.RawDataType = Globals.RawDataType.Centroided;
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
Console.WriteLine("Num XY datapoints in mass spectrum= " + run.XYData.Xvalues.Length);
Console.WriteLine("numPeaks = " + run.PeakList.Count);
Assert.AreEqual(run.XYData.Xvalues.Length, run.PeakList.Count);
//TestUtilities.DisplayXYValues(run.XYData);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void PeakDetectorOnCentroidedDataTest2()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6006); //this is a MS2 scan
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
// Note that setting the PeakFitType to Apex will not matter since RawDataType is Centroided
// It would only matter if the RawDataType was Profile
var peakDetector = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.APEX, true);
peakDetector.RawDataType = Globals.RawDataType.Centroided;
peakDetector.SignalToNoiseThreshold = 0;
peakDetector.PeakToBackgroundRatio = 0;
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
Console.WriteLine("Num XY datapoints in mass spectrum= " + run.XYData.Xvalues.Length);
Console.WriteLine("numPeaks = " + run.PeakList.Count);
Assert.AreEqual(run.XYData.Xvalues.Length, run.PeakList.Count);
//TestUtilities.DisplayXYValues(run.XYData);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void CheckBackgroundIntensityTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6005);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
peakDetector.SignalToNoiseThreshold = 2;
peakDetector.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakDetector.IsDataThresholded = true;
var oldPeakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
oldPeakDetector.Execute(run.ResultCollection);
//Assert.AreEqual(peakDetector.BackgroundIntensity, oldPeakDetector.BackgroundIntensity);
}
public void DetectPeaksInOrbitrapData()
{
var peakBR = 1.3;
double sigNoise = 2;
var isThresholded = true;
var peakfitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
Run run = new XCaliburRun2(testFile);
//create list of target scansets
run.ScanSetCollection.Create(run, 6000, 6015, 1, 1);
//in the 'run' object there is now a list of scans : run.ScanSetCollection
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2(peakBR, sigNoise, peakfitType, isThresholded);
peakDet.PeaksAreStored = true;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
//set the target scan:
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
public void SpeedTest1()
{
var fileName = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 5500, 5550, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakBr = 1.3;//0.25;
var peakDetector = new DeconToolsPeakDetectorV2(peakBr, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = peakBr;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var watch = new Stopwatch();
watch.Start();
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
newDeconvolutor.Execute(run.ResultCollection);
}
watch.Stop();
Console.WriteLine("Time per scan (INFORMED) = " + watch.ElapsedMilliseconds / run.ScanSetCollection.ScanSetList.Count);
}
public void Test1()
{
string testfile = @"D:\Data\From_Nicola\AC2_Neg_highpH_14Apr13_Sauron_13-04-03.raw";
Run run = new RunFactory().CreateRun(testfile);
TestUtilities.DisplayRunInformation(run);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
ScanSet scanSet = new ScanSet(4100);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.Execute(run.ResultCollection);
run.PeakList = run.PeakList.Where(p => p.XValue > 742 && p.XValue < 749).ToList();
HornDeconvolutor hornDeconvolutor = new HornDeconvolutor();
hornDeconvolutor.ChargeCarrierMass = -1.00727649;
hornDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public static Run CreateResultsFromThreeScansOfStandardOrbitrapData()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6000, 6020, 1, 1, false);
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
}
return(run);
}
public void Test1()
{
var peakAssociator = new PeakToMSFeatureAssociator();
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
peakAssociator.Execute(run.ResultCollection);
var numPeaksAssociatedWithFeatures = 0;
foreach (var msfeature in run.ResultCollection.ResultList)
{
foreach (var peak in msfeature.IsotopicProfile.Peaklist)
{
numPeaksAssociatedWithFeatures++;
}
}
var numPeaksInPeakListWithAssociations = 0;
foreach (MSPeak peak in run.PeakList)
{
Console.WriteLine(peak.MSFeatureID + "\t" + peak.XValue + "\t" + peak.Height + "\t");
if (peak.MSFeatureID != -1)
{
numPeaksInPeakListWithAssociations++;
}
}
//I don't think I can assume this... msfeature1 might overlap and share a peak with msfeature2
//Assert.AreEqual(numPeaksAssociatedWithFeatures, numPeaksInPeakListWithAssociations);
Console.WriteLine("total peaks associated with MSFeatures = " + numPeaksAssociatedWithFeatures);
Console.WriteLine("total peaks in original peaklist that were associated = " + numPeaksInPeakListWithAssociations);
Console.WriteLine("fraction peaks assigned = " + (double)(numPeaksInPeakListWithAssociations / (double)run.PeakList.Count));
}
public void OldDeconvolutorOrbitrapTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6005, 6200, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var deconvolutor = new HornDeconvolutor();
deconvolutor.MinPeptideBackgroundRatio = 3;
//deconvolutor.IsMZRangeUsed = true;
//deconvolutor.MinMZ = 575;
//deconvolutor.MaxMZ = 585;
foreach (var scanSet in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
var stopwatch = new Stopwatch();
stopwatch.Start();
deconvolutor.Execute(run.ResultCollection);
stopwatch.Stop();
Console.WriteLine("Time for decon= \t" + stopwatch.ElapsedMilliseconds);
}
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
////order and get the most intense msfeature
//run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IsotopicProfile.IntensityAggregate).ToList();
//IsosResult testIso = run.ResultCollection.ResultList[0];
//Assert.AreEqual(13084442, testIso.IsotopicProfile.IntensityAggregate);
//Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
//Assert.AreEqual(0.01012m, (decimal)Math.Round(testIso.IsotopicProfile.Score, 5));
//Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
//Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
//Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
//Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
//TestUtilities.DisplayIsotopicProfileData(testIso.IsotopicProfile);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void ComparePeakFitterVsAreaFitter()
{
var massTagFile1 = Path.Combine(FileRefs.RawDataBasePath, "TargetedWorkflowStandards", "QCShew_peptidesWithObsCountGreaterThan1000.txt");
//load target
var masstagImporter = new MassTagFromTextFileImporter(massTagFile1);
var targets = masstagImporter.Import().TargetList;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var scanSet = new ScanSet(9575);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var selectedTarget = targets.First(p => p.ID == 635428 && p.ChargeState == 3);
var theorFeatureGen = new JoshTheorFeatureGenerator(Backend.Globals.LabellingType.NONE, 0.005);
theorFeatureGen.GenerateTheorFeature(selectedTarget);
var peakForFWHM = run.PeakList.First(p => p.XValue > 768.38 && p.XValue < 768.39);
var theorXYdata =
TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData(selectedTarget.IsotopicProfile,
peakForFWHM.Width);
theorXYdata.NormalizeYData();
var areaFitter = new AreaFitter();
var areaFitScore = areaFitter.GetFit(theorXYdata, run.XYData, 0.1);
var peakLeastSquaresFitter = new PeakLeastSquaresFitter();
var peakBasedFitScore = peakLeastSquaresFitter.GetFit(new List <Peak>(selectedTarget.IsotopicProfile.Peaklist), run.PeakList, 0.1, 25);
Console.WriteLine("fit score based on XYData = " + areaFitScore);
Console.WriteLine("fit score based on Peaks= " + peakBasedFitScore);
Assert.IsTrue(peakBasedFitScore < 0.1);
}
public void ThrashPreferPlusOneChargeStateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6005, 6005, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(0.5, 2, Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
var parameters = new ThrashParameters();
parameters.MinMSFeatureToBackgroundRatio = 1;
parameters.MaxFit = 0.3;
parameters.CheckAllPatternsAgainstChargeState1 = true;
var deconvolutor = new ThrashDeconvolutorV2(parameters);
var scan = new ScanSet(6005);
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.PeakList = run.PeakList.Where(p => p.XValue > 750 && p.XValue < 753).ToList();
deconvolutor.Execute(run.ResultCollection);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
var result1 = run.ResultCollection.ResultList.First();
Assert.AreEqual(1, result1.IsotopicProfile.ChargeState);
Console.WriteLine("--------- Prefer +1 charge state ----------------");
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
run.ResultCollection.ResultList.Clear();
run.ResultCollection.IsosResultBin.Clear();
deconvolutor.Parameters.CheckAllPatternsAgainstChargeState1 = false;
deconvolutor.Execute(run.ResultCollection);
Console.WriteLine("\n--------- No charge state bias ----------------");
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
result1 = run.ResultCollection.ResultList.First();
Assert.AreEqual(3, result1.IsotopicProfile.ChargeState);
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
var deconParameters = new DeconToolsParameters();
deconParameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 2; // PeptideMinBackgroundRatio
Task decon = new HornDeconvolutor(deconParameters);
decon.Execute(results);
var result1 = results.ResultList[0];
var distcreator = new MercuryDistributionCreator();
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var theorXYData = distcreator.Data;
//StringBuilder sb = new StringBuilder();
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(579, 582, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[1];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
var sb = new StringBuilder();
var theorXYData = distcreator.Data;
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
distcreator.OffsetDistribution(result1.IsotopicProfile);
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0763818319332606m, (decimal)fitval);
}
public void ValidateDataTest_temp() //purpose is to compare
{
var testMz5File = @"C:\Sipper\SipperDemo\RawDataFiles\Yellow_C13_070_23Mar10_Griffin_10-01-28.mz5";
var testThermoFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
var mz5run = new RunFactory().CreateRun(testMz5File);
mz5run.IsDataThresholded = true;
var thermoRun = new RunFactory().CreateRun(testThermoFile);
var testScanMz5 = 6010;
var testScanThermo = 6011;
var testScanSet1 = new ScanSet(testScanMz5);
var testScanSetThermo = new ScanSet(testScanThermo);
mz5run.CurrentScanSet = testScanSet1;
thermoRun.CurrentScanSet = testScanSetThermo;
mz5run.GetMassSpectrum(testScanSet1);
thermoRun.GetMassSpectrum(testScanSetThermo);
Assert.AreEqual(mz5run.XYData.Xvalues.Length, thermoRun.XYData.Xvalues.Length);
for (var i = 0; i < mz5run.XYData.Xvalues.Length; i++)
{
Assert.AreEqual(mz5run.XYData.Xvalues[i], thermoRun.XYData.Xvalues[i]);
}
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 3;
peakDetector.SignalToNoiseThreshold = 2;
peakDetector.Execute(mz5run.ResultCollection);
//peakDetector.Execute(thermoRun.ResultCollection);
TestUtilities.DisplayPeaks(mz5run.PeakList);
Console.WriteLine();
Console.WriteLine();
// TestUtilities.DisplayPeaks(thermoRun.PeakList);
}
public void fitterOnRapidDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
bool isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
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 DeconToolsPeakDetectorV2(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
// theorXYData.Display();
AreaFitter areafitter = new AreaFitter();
double fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval);
}
public void smootherTest1()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
Task msgen = new GenericMSGenerator();
msgen.Execute(run.ResultCollection);
var peakdetector = new DeconToolsPeakDetectorV2(3, 3, Globals.PeakFitType.QUADRATIC, true);
peakdetector.Execute(run.ResultCollection);
Assert.AreEqual(84, run.PeakList.Count);
Task smoother = new SavitzkyGolaySmoother(7, 2, false);
smoother.Execute(run.ResultCollection);
peakdetector.Execute(run.ResultCollection);
Assert.AreEqual(46, run.PeakList.Count);
}
public void CompareToScottsData1()
{
var fileName = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var run = new RunFactory().CreateRun(fileName);
run.ScanSetCollection.Create(run, 5509, 5509, 1, 1, false);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakBr = 1.9;//1.3;
var peakDetector = new DeconToolsPeakDetectorV2(peakBr, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = peakBr;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new InformedThrashDeconvolutor(thrashParameters);
var scanset = new ScanSet(5509);
run.CurrentScanSet = scanset;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
run.CurrentScanSet.BackgroundIntensity = peakDetector.BackgroundIntensity;
newDeconvolutor.Execute(run.ResultCollection);
var scottMzVals = ReadScottsAnnotationsScan5509().ToArray();
var myMzVals = run.ResultCollection.ResultList.Select(p => p.IsotopicProfile.MonoPeakMZ).OrderBy(p => p).ToArray();
var comparisions = new Dictionary <decimal, double>();
foreach (var scottVal in scottMzVals)
{
var tolerance = 0.01;
var indexInThrash = MathUtils.BinarySearchWithTolerance(myMzVals, scottVal, 0, myMzVals.Length - 1, tolerance);
var myMzVal = indexInThrash == -1 ? 0.0d : myMzVals[indexInThrash];
comparisions.Add((decimal)scottVal, myMzVal);
}
var numCorrect = comparisions.Values.Count(p => p > 0);
var numMissing = scottMzVals.Count() - numCorrect;
Console.WriteLine("Total annotated= \t" + scottMzVals.Count());
Console.WriteLine("Number correct = \t" + numCorrect);
Console.WriteLine("Number missing = \t" + numMissing);
}
public void Test1()
{
var rawfilename = @"D:\Data\O16O18\GlueGrant\GG_MO_Trauma_374020_20May11_Sphinx_11-03-28.RAW";
var exportedIsos = Path.Combine(Path.GetDirectoryName(rawfilename), Path.GetFileName(rawfilename).Replace(".RAW", "_test_isos.csv"));
if (File.Exists(exportedIsos))
{
File.Delete(exportedIsos);
}
var run = new RunFactory().CreateRun(rawfilename);
run.ResultCollection.ResultType = Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 5000, 5000, 1, 1);
run.CurrentScanSet = run.ScanSetCollection.ScanSetList[0];
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 1.3;
peakDet.SignalToNoiseThreshold = 2;
var decon = new HornDeconvolutor();
decon.IsO16O18Data = true;
var appender = new O16O18PeakDataAppender();
var exporter = IsosExporterFactory.CreateIsosExporter(run.ResultCollection.ResultType, Backend.Globals.ExporterType.Text, exportedIsos);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
appender.Execute(run.ResultCollection);
var testResult = (O16O18IsosResult)run.ResultCollection.ResultList[1];
Assert.AreEqual(DeconTools.Backend.Globals.ResultType.O16O18_TRADITIONAL_RESULT, run.ResultCollection.ResultType);
Assert.AreEqual(5905390, testResult.IsotopicProfile.GetMonoAbundance());
Assert.AreEqual(3017899, testResult.MonoPlus2Abundance);
Assert.AreEqual(162389, testResult.MonoPlus4Abundance);
exporter.Execute(run.ResultCollection);
run.Close();
}
public void ValidateDataTest1() //purpose is to compare
{
var testMz5File = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\mzXML\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.mz5";
var testThermoFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var mz5run = new RunFactory().CreateRun(testMz5File);
var thermoRun = new RunFactory().CreateRun(testThermoFile);
var testScanMz5 = 6004;
var testScanThermo = 6005;
var testScanSet1 = new ScanSet(testScanMz5);
var testScanSetThermo = new ScanSet(testScanThermo);
mz5run.CurrentScanSet = testScanSet1;
thermoRun.CurrentScanSet = testScanSetThermo;
mz5run.XYData = mz5run.GetMassSpectrum(testScanSet1);
thermoRun.XYData = thermoRun.GetMassSpectrum(testScanSetThermo);
Assert.AreEqual(mz5run.XYData.Xvalues.Length, thermoRun.XYData.Xvalues.Length);
for (var i = 0; i < mz5run.XYData.Xvalues.Length; i++)
{
Assert.AreEqual(mz5run.XYData.Xvalues[i], thermoRun.XYData.Xvalues[i]);
}
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 3;
peakDetector.SignalToNoiseThreshold = 2;
//peakDetector.Execute(mz5run.ResultCollection);
peakDetector.Execute(thermoRun.ResultCollection);
//TestUtilities.DisplayPeaks(mz5run.PeakList);
Console.WriteLine();
Console.WriteLine();
TestUtilities.DisplayPeaks(thermoRun.PeakList);
}
public void peak_interference_weakFeature_test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 597 && p.IsotopicProfile.MonoPeakMZ < 598).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public void interference_allFeaturesInScan_test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
foreach (var isosResult in run.ResultCollection.ResultList)
{
var monoPeak = isosResult.IsotopicProfile.getMonoPeak();
var lastPeak = isosResult.IsotopicProfile.Peaklist[isosResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var interferenceScore = interferenceScorer.GetInterferenceScore(run.XYData, isosResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width, startIndexOfXYData);
stopwatch.Stop();
Console.WriteLine("interference= \t" + interferenceScore);
}
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void ThrashV2OnIMSDataTest1()
{
var uimfFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var zeroFiller = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3);
var thrashParameters = new ThrashParameters();
thrashParameters.MinMSFeatureToBackgroundRatio = 1;
thrashParameters.MaxFit = 0.4;
var newDeconvolutor = new ThrashDeconvolutorV2(thrashParameters);
var testLCScan = 500;
var testIMSScan = 120;
var numIMSScanSummed = 7;
var lowerIMSScan = testIMSScan - (numIMSScanSummed - 1) / 2;
var upperIMSScan = testIMSScan + (numIMSScanSummed - 1) / 2;
var scanSet = new ScanSetFactory().CreateScanSet(run, testLCScan, 1);
run.CurrentScanSet = scanSet;
((UIMFRun)run).CurrentIMSScanSet = new IMSScanSet(testIMSScan, lowerIMSScan, upperIMSScan);
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
newDeconvolutor.Execute(run.ResultCollection);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Assert.IsTrue(run.ResultCollection.ResultList.Count > 0);
Assert.AreEqual(33, run.ResultCollection.ResultList.Count);
var result1 = run.ResultCollection.ResultList[0];
Assert.AreEqual(13084442, (decimal)Math.Round(result1.IntensityAggregate));
Assert.AreEqual(960.53365m, (decimal)Math.Round(result1.IsotopicProfile.MonoIsotopicMass, 5));
Assert.AreEqual(2, result1.IsotopicProfile.ChargeState);
}
