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 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);
}
protected virtual void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//the new iThrash imports the _peaks.txt file
if (Deconvolutor is DeconTools.Backend.ProcessingTasks.Deconvoluters.InformedThrashDeconvolutor)
{
_deconvolutorRequiresPeaksFile = true;
}
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ScanResultUpdater = new ScanResultUpdater(NewDeconToolsParameters.ScanBasedWorkflowParameters.ProcessMS2);
ResultValidator = new ResultValidatorTask();
IsosResultExporter = IsosExporterFactory.CreateIsosExporter(Run.ResultCollection.ResultType, ExporterType,
IsosOutputFileName);
ScanResultExporter = ScansExporterFactory.CreateScansExporter(Run.MSFileType, ExporterType,
ScansOutputFileName);
if (!_deconvolutorRequiresPeaksFile)
{
PeakListExporter = PeakListExporterFactory.Create(ExporterType, Run.MSFileType, PeakListExporterTriggerValue,
PeakListOutputFileName);
}
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
}
public SmartChromPeakSelector(SmartChromPeakSelectorParameters parameters)
{
this.Parameters = parameters;
MSPeakDetector = new DeconToolsPeakDetectorV2(parameters.MSPeakDetectorPeakBR, parameters.MSPeakDetectorSigNoiseThresh, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var iterativeTFFParams = new IterativeTFFParameters();
iterativeTFFParams.ToleranceInPPM = parameters.MSToleranceInPPM;
iterativeTFFParams.MinimumRelIntensityForForPeakInclusion = parameters.IterativeTffMinRelIntensityForPeakInclusion;
if (parameters.MSFeatureFinderType == DeconTools.Backend.Globals.TargetedFeatureFinderType.BASIC)
{
throw new NotSupportedException("Currently the Basic TFF is not supported in the SmartChromPeakSelector");
//TargetedMSFeatureFinder = new TargetedFeatureFinders.BasicTFF(parameters.MSToleranceInPPM);
}
else
{
TargetedMSFeatureFinder = new IterativeTFF(iterativeTFFParams);
}
resultValidator = new ResultValidatorTask();
fitScoreCalc = new IsotopicProfileFitScoreCalculator();
InterferenceScorer = new InterferenceScorer();
}
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);
}
protected virtual void DoMainInitialization()
{
ValidateParameters();
TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromGen = new PeakChromatogramGenerator(WorkflowParameters.ChromGenTolerance, WorkflowParameters.ChromGeneratorMode,
DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED,
WorkflowParameters.ChromGenToleranceUnit)
{
TopNPeaksLowerCutOff = 0.333,
ChromWindowWidthForAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2,
ChromWindowWidthForNonAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2
};
//only
var allowNegativeValues = false;
ChromSmoother = new SavitzkyGolaySmoother(WorkflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues);
ChromPeakDetector = new ChromPeakDetector(WorkflowParameters.ChromPeakDetectorPeakBR, WorkflowParameters.ChromPeakDetectorSigNoise);
ChromPeakSelector = CreateChromPeakSelector(WorkflowParameters);
ChromPeakAnalyzer = new ChromPeakAnalyzer(WorkflowParameters);
IterativeTffParameters = new IterativeTFFParameters();
IterativeTffParameters.ToleranceInPPM = WorkflowParameters.MSToleranceInPPM;
MsfeatureFinder = new IterativeTFF(IterativeTffParameters);
FitScoreCalc = new IsotopicProfileFitScoreCalculator();
InterferenceScorer = new InterferenceScorer();
ResultValidator = new ResultValidatorTask();
ChromatogramCorrelator = new IqChromCorrelator(WorkflowParameters.ChromSmootherNumPointsInSmooth, 0.05, WorkflowParameters.ChromGenTolerance);
}
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);
}
protected override void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
var moreSensitivePeakToBackgroundRatio = NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio / 2;
var moreSensitiveSigNoiseThresh = NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold;
_moreSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(moreSensitivePeakToBackgroundRatio,
moreSensitiveSigNoiseThresh, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
_superSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(0, 0, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ResultValidator = new ResultValidatorTask();
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
_ms2PeakDetectorForCentroidData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true)
{
RawDataType = Globals.RawDataType.Centroided
};
_ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio,
NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold,
NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Check.Ensure(Deconvolutor is ThrashDeconvolutorV2, "Error. Currently the DeconMSn workflow only works with the ThrashV2 deconvolutor. Selected deconvolutor= " + Deconvolutor);
}
public void outputToText_xcaliburData_Test2()
{
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();
BasicIsosResultTextFileExporter isosExporter = new BasicIsosResultTextFileExporter(testFile);
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);
}
isosExporter.ExportIsosResults(run.ResultCollection.ResultList);
Assert.AreEqual(true, File.Exists(testFile));
FileInfo fi = new FileInfo(testFile);
//Assert.AreEqual(25881, fi.Length);
Console.Write(fi.Length);
}
//public override WorkflowParameters WorkflowParameters
//{
// get
// {
// throw new NotImplementedException();
// }
// set
// {
// throw new NotImplementedException();
// }
//}
public void InitializeWorkflow()
{
this.ChromGenToleranceInPPM = 20;
this.ChromGenerator = new ChromatogramGenerator();
this.ChromSmoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2);
this.ChromPeakDetector = new ChromPeakDetector(0.5, 0.5);
this.MSPeakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false);
// To include support for Rapid, you must add a reference to DeconEngine.dll, which was compiled with Visual Studio 2003 and uses MSVCP71.dll
// Note that DeconEngine.dll also depends on xerces-c_2_7.dll while DeconEngineV2.dll depends on xerces-c_2_8.dll
#if INCLUDE_RAPID
this.Deconvolutor = new RapidDeconvolutor();
Validator = new ResultValidatorTask();
isosExporter = new DeconTools.Backend.FileIO.MSFeatureToTextFileExporterBasic(m_isosResultFileName);
#else
throw new NotSupportedException("Support for Rapid is not included in this version of the DLL");
#endif
}
protected virtual void DoMainInitialization()
{
ValidateParameters();
_theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
_chromGen = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode,
DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED,
_workflowParameters.ChromGenToleranceUnit)
{
TopNPeaksLowerCutOff = 0.333,
ChromWindowWidthForAlignedData = (float)_workflowParameters.ChromNETTolerance * 2,
ChromWindowWidthForNonAlignedData = (float)_workflowParameters.ChromNETTolerance * 2
};
//only
var allowNegativeValues = false;
_chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues);
_chromPeakDetector = new ChromPeakDetectorMedianBased(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise);
_chromPeakSelector = CreateChromPeakSelector(_workflowParameters);
_iterativeTFFParameters = new IterativeTFFParameters();
_iterativeTFFParameters.ToleranceInPPM = _workflowParameters.MSToleranceInPPM;
_msfeatureFinder = new IterativeTFF(_iterativeTFFParameters);
_fitScoreCalc = new IsotopicProfileFitScoreCalculator();
_resultValidator = new ResultValidatorTask();
_chromatogramCorrelator = new ChromatogramCorrelator(_workflowParameters.ChromSmootherNumPointsInSmooth, 0.01, _workflowParameters.ChromGenTolerance);
ChromatogramXYData = new XYData();
MassSpectrumXYData = new XYData();
ChromPeaksDetected = new List <ChromPeak>();
}
public static Run CreateResultsFromTwoFramesOfStandardUIMFData()
{
var run = new UIMFRun(FileRefs.RawDataMSFiles.UIMFStdFile1);
run.ResultCollection.ResultType = Globals.ResultType.UIMF_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 500, 501, 3, 1);
run.IMSScanSetCollection.Create(run, 250, 270, 9, 1);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task driftTimeextractor = new UIMFDriftTimeExtractor();
foreach (var frame in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = frame;
foreach (IMSScanSet scan in run.IMSScanSetCollection.ScanSetList)
{
run.CurrentIMSScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeextractor.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
}
}
return(run);
}
public static Run CreatePeakDataFromStandardOrbitrapData()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
run.ScanSetCollection.Create(run, 6000, 6050, 1, 1, false);
Task msgen = new GenericMSGenerator();
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeaksAreStored = true;
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);
}
return(run);
}
public void outputToText_uimf_test1()
{
if (File.Exists(uimf_text_IsosResultOutputFile1))
{
File.Delete(uimf_text_IsosResultOutputFile1);
}
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 240, 9, 1, false);
sscc.Create();
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fsc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.UIMFIsosResultTextFileExporter(uimf_text_IsosResultOutputFile1, 1000000);
Task flagger = new ResultValidatorTask();
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);
flagger.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
isosExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
Assert.AreEqual(true, File.Exists(uimf_text_IsosResultOutputFile1));
FileInfo fi = new FileInfo(uimf_text_IsosResultOutputFile1);
Assert.AreEqual(99743, fi.Length);
Console.Write(fi.Length);
}
protected override void DoPostInitialization()
{
base.DoPostInitialization();
ValidateParameters();
theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
theorN15FeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
chromGenN14 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode);
chromGenN14.TopNPeaksLowerCutOff = 0.333;
chromGenN15 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, DeconTools.Backend.Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK, DeconTools.Backend.Globals.IsotopicProfileType.LABELLED);
chromGenN15.TopNPeaksLowerCutOff = 0.333;
var pointsToSmooth = (_workflowParameters.ChromSmootherNumPointsInSmooth + 1) / 2;
chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2);
chromPeakDetector = new ChromPeakDetector(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise);
var smartchrompeakSelectorParams = new SmartChromPeakSelectorParameters();
smartchrompeakSelectorParams.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE;
smartchrompeakSelectorParams.MSPeakDetectorPeakBR = _workflowParameters.MSPeakDetectorPeakBR;
smartchrompeakSelectorParams.MSPeakDetectorSigNoiseThresh = _workflowParameters.MSPeakDetectorSigNoise;
smartchrompeakSelectorParams.MSToleranceInPPM = _workflowParameters.MSToleranceInPPM;
smartchrompeakSelectorParams.NETTolerance = (float)_workflowParameters.ChromNETTolerance;
smartchrompeakSelectorParams.NumScansToSum = _workflowParameters.NumMSScansToSum;
smartchrompeakSelectorParams.NumChromPeaksAllowed = 10;
smartchrompeakSelectorParams.IterativeTffMinRelIntensityForPeakInclusion = 0.5;
chromPeakSelectorN14 = new SmartChromPeakSelector(smartchrompeakSelectorParams);
var chromPeakSelectorParameters = new ChromPeakSelectorParameters();
chromPeakSelectorParameters.NumScansToSum = _workflowParameters.NumMSScansToSum;
chromPeakSelectorParameters.NETTolerance = (float)_workflowParameters.ChromNETTolerance;
chromPeakSelectorParameters.PeakSelectorMode = DeconTools.Backend.Globals.PeakSelectorMode.N15IntelligentMode;
chromPeakSelectorN15 = new BasicChromPeakSelector(chromPeakSelectorParameters);
chromPeakSelectorN15.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED;
msPeakDetector = new DeconToolsPeakDetectorV2(_workflowParameters.MSPeakDetectorPeakBR,
_workflowParameters.MSPeakDetectorSigNoise, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false);
var iterativeTFFParameters = new IterativeTFFParameters();
iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM;
iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33;
iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED;
unlabelledProfilefinder = new IterativeTFF(iterativeTFFParameters);
iterativeTFFParameters = new IterativeTFFParameters();
iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM;
iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33;
iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED;
labelledProfileFinder = new IterativeTFF(iterativeTFFParameters);
quantifier = new N14N15QuantifierTask(_n14N15Workflow2Parameters.NumPeaksUsedInQuant, _workflowParameters.MSToleranceInPPM);
fitScoreCalc = new IsotopicProfileFitScoreCalculator();
var minRelativeIntensityForScore = 0.2;
resultValidatorN14 = new ResultValidatorTask(minRelativeIntensityForScore, true);
resultValidatorN15 = new LabelledIsotopicProfileScorer(minRelativeIntensityForScore);
ChromatogramXYData = new XYData();
MassSpectrumXYData = new XYData();
ChromPeaksDetected = new List <ChromPeak>();
}
