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>(); }