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);
}
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>();
}
