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>();
}
