public SipperQuantifier() { ChromToleranceInPPM = 25; NumPointsInSmoother = 7; MinimumRelativeIntensityForChromCorr = 0.0001; _chromatogramCorrelatorTask = new ChromatogramCorrelator(NumPointsInSmoother, MinimumRelativeIntensityForChromCorr, (int)ChromToleranceInPPM); _labelingDistributionCalculator = new LabelingDistributionCalculator(); _partialLabelingQuantifier = new PartialLabelingQuantifier("C", 12, 13) { MaxLabelAmount = 15, StepAmountForIterator = 0.25, NumLeftZeroPads = 1, NumRightZeroPads = 1, IsTheoreticalTrimmedDownToObserved = true }; IsChromatogramCorrelationPerformed = true; MaximumFitScoreForFurtherProcessing = 0.50; MinimumRatioAreaForFurtherProcessing = 5; MinimumRSquaredValForQuant = 0.75; ChromatogramRSquaredVals = new List <double>(); RatioVals = new XYData(); FitScoreData = new Dictionary <decimal, double>(); }
public SipperQuantifierOld() { IsChromatogramCorrelationPerformed = true; MaximumFitScoreForFurtherProcessing = 0.50; MinimumRatioAreaForFurtherProcessing = 5; MinimumRSquaredValForQuant = 0.75; MinimumRelativeIntensityForChromCorr = 0.0001; ChromToleranceInPPM = 25; const int numPointsInSmoother = 5; _chromatogramCorrelatorTask = new ChromatogramCorrelator(numPointsInSmoother, MinimumRelativeIntensityForChromCorr, (int)ChromToleranceInPPM); ChromatogramRSquaredVals = new List <double>(); RatioLogVals = new XYData(); RatioVals = new XYData(); _labelingDistributionCalculator = new LabelingDistributionCalculator(); _partialLabelingQuantifier = new PartialLabelingQuantifier("C", 12, 13); _partialLabelingQuantifier.MaxLabelAmount = 15; _partialLabelingQuantifier.StepAmountForIterator = 0.25; }
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>(); }