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 getPeakChromatogramTest2()
{
var mt = TestUtilities.GetMassTagStandard(1);
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(10, Globals.ChromatogramGeneratorMode.TOP_N_PEAKS);
peakChromGen.TopNPeaksLowerCutOff = 0.4;
peakChromGen.Execute(run.ResultCollection);
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
//Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
run.XYData.Display();
}
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 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 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 processOrbiWithNewWorkflowTest2()
{
var minScan = 5500;
var maxScan = 6500;
Run run = new XCaliburRun2(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1, minScan, maxScan);
var workflow = new WholisticChromBasedLCMSFeatureFinderWorkflow(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
//run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan).ToList();
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
var sw = new Stopwatch();
sw.Start();
workflow.Execute();
sw.Stop();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
Console.WriteLine("workflow time = " + sw.ElapsedMilliseconds);
}
public void processOrbi_Refining_Case01_whatHappensTo_PeakID_396293()
{
var minScan = 200;
var maxScan = 18000;
Run run = new XCaliburRun2(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var workflow = new WholisticChromBasedLCMSFeatureFinderWorkflow(run);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile1);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
#if peaksAreFilteredToNarrowMZ
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
#else
run.ResultCollection.MSPeakResultList = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan).ToList();
#endif
workflow.Execute();
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
var filteredPeakResults = run.ResultCollection.MSPeakResultList.Where(p => p.Scan_num > minScan && p.Scan_num < maxScan && p.MSPeak.XValue > 771 && p.MSPeak.XValue < 775).ToList();
//TestUtilities.DisplayMSPeakResults(filteredPeakResults);
}
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 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 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 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 TempTest1()
{
using (var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1))
{
run.GetTuneData();
}
}
public void DetectPeaksTest1()
{
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);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
var peakDet = new DeconToolsPeakDetectorV2(peakBR, sigNoise, peakfitType, isThresholded);
peakDet.PeaksAreStored = true;
var peakList = peakDet.FindPeaks(run.XYData, 0, 50000);
TestUtilities.DisplayPeaks(peakList);
}
public void checkDataSetNamesAndPathsTest()
{
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
Run run = new XCaliburRun2(testFile);
Assert.AreEqual("QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18", run.DatasetName);
}
public void checkVersion_2pt2_xcalibur_dll_test1()
{
var run = new XCaliburRun2(@"\\proto-7\VOrbiETD01\2012_3\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08.raw");
Assert.AreEqual(8904, run.GetNumMSScans());
Assert.IsNotNull(run);
}
public void ConstructorTest1()
{
using (Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1))
{
Assert.AreEqual(1, run.MinLCScan);
Assert.AreEqual(18505, run.MaxLCScan);
}
}
public void ConstructorTest2()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1, 6000, 7000);
Assert.AreEqual(6000, run.MinLCScan);
Assert.AreEqual(7000, run.MaxLCScan);
run = null;
}
public void initializeVelosOrbiFile_Test1()
{
var testFile = FileRefs.RawDataMSFiles.VOrbiFile1;
Run run = new XCaliburRun2(testFile);
Assert.AreEqual(1, run.MinLCScan);
Assert.AreEqual(17773, run.MaxLCScan);
}
public void GetTICFromInstrumentInfoTest1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = 6005;
var ticIntensity = run.GetTICFromInstrumentInfo(scan);
Assert.IsTrue(ticIntensity > 0);
}
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 GetIonInjectionTimeTest1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = 6005;
var ionInjectionTime = run.GetIonInjectionTimeInMilliseconds(scan);
Assert.AreEqual(2.84m, (decimal)Math.Round(ionInjectionTime, 2));
Console.WriteLine("Scan " + scan + "; ion injection time = " + ionInjectionTime);
}
public void getSpectrum_Test1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var xydata = run.GetMassSpectrum(new Backend.Core.ScanSet(6005));
Assert.IsTrue(xydata.Xvalues.Length > 1000);
// TestUtilities.DisplayXYValues(xydata);
}
public void GetMS2IsolationWidthTest1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = 6006;
var isolationWidth = run.GetMS2IsolationWidth(scan);
Assert.AreEqual(3.0m, (decimal)Math.Round(isolationWidth, 1));
Console.WriteLine("Scan " + scan + "; MS2IsolationWidth = " + isolationWidth);
}
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 getSummedSpectrum_Test1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scanset = new ScanSet(6005, new int[] { 6005, 6012, 6019 });
var xydata = run.GetMassSpectrum(scanset);
Assert.IsTrue(xydata.Xvalues.Length > 1000);
//TestUtilities.DisplayXYValues(run.XYData);
}
public void GetScanInfoTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var msmsScanNum1 = 6000;
var scan = new ScanSet(msmsScanNum1);
var scanInfoString = run.GetScanInfo(scan.PrimaryScanNumber);
Assert.AreEqual(@"ITMS + c NSI d Full ms2 [email protected] [135.00-2000.00]", scanInfoString);
}
public void getNumSpectraTest1()
{
var run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var numScans = run.GetNumMSScans();
Assert.AreEqual(18505, numScans);
Assert.AreEqual(1, run.MinLCScan);
Assert.AreEqual(18505, run.MaxLCScan);
//TestUtilities.DisplayXYValues(run.XYData);
}
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 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 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
}
