public IterativeTFF(IterativeTFFParameters parameters)
{
PeakBRStep = parameters.PeakBRStep;
_peakDetectorIsDataThresholded = parameters.PeakDetectorIsDataThresholded;
_peakDetectorSigNoiseRatioThreshold = parameters.PeakDetectorSigNoiseRatioThreshold;
PeakDetectorPeakBR = parameters.PeakDetectorPeakBR;
_peakDetectorPeakFitType = parameters.PeakDetectorPeakFitType;
PeakBRMin = parameters.PeakDetectorMinimumPeakBR;
MaxPeaksToInclude = 30;
MinRelIntensityForPeakInclusion = parameters.MinimumRelIntensityForForPeakInclusion;
this.NeedMonoIsotopicPeak = parameters.RequiresMonoIsotopicPeak;
this.ToleranceInPPM = parameters.ToleranceInPPM;
this.NumPeaksUsedInAbundance = parameters.NumPeaksUsedInAbundance;
this.IsotopicProfileType = parameters.IsotopicProfileType;
this.MSPeakDetector = new DeconToolsPeakDetectorV2(PeakDetectorPeakBR, _peakDetectorSigNoiseRatioThreshold,
_peakDetectorPeakFitType, _peakDetectorIsDataThresholded);
//this.MSPeakDetector = new DeconToolsPeakDetectorV2();
//this.MSPeakDetector.PeakToBackgroundRatio = PeakDetectorPeakBR;
//this.MSPeakDetector.SignalToNoiseThreshold = _peakDetectorSigNoiseRatioThreshold;
//this.MSPeakDetector.IsDataThresholded = _peakDetectorIsDataThresholded;
//this.MSPeakDetector.PeakFitType = _peakDetectorPeakFitType;
}
public DeconToolsPeakDetector(double peakToBackgroundRatio, double signalToNoiseRatio, Globals.PeakFitType peakFitType, bool isDataThresholded, double minX = 0, double maxX = double.MaxValue)
{
PeakToBackgroundRatio = peakToBackgroundRatio;
SignalToNoiseThreshold = signalToNoiseRatio;
PeakFitType = peakFitType;
IsDataThresholded = isDataThresholded;
MaxX = maxX;
MinX = minX;
}
public DeconToolsPeakDetectorV2(double peakToBackgroundRatio,
double signalToNoiseThreshold,
Globals.PeakFitType peakFitType = Globals.PeakFitType.QUADRATIC,
bool isDataThresholded = false)
{
PeakToBackgroundRatio = peakToBackgroundRatio;
SignalToNoiseThreshold = signalToNoiseThreshold;
PeakFitType = peakFitType;
IsDataThresholded = isDataThresholded;
}
public override void LoadParametersV2(XElement xElement)
{
PeakToBackgroundRatio = GetDoubleValue(xElement, "PeakBackgroundRatio", PeakToBackgroundRatio);
SignalToNoiseThreshold = GetDoubleValue(xElement, "SignalToNoiseThreshold", SignalToNoiseThreshold);
IsDataThresholded = GetBoolVal(xElement, "IsDataThresholded", IsDataThresholded);
PeakFitType = (Globals.PeakFitType)GetEnum(xElement, "PeakFitType", PeakFitType.GetType(), PeakFitType);
//TODO: move this parameter
PeaksAreStored = GetBoolVal(xElement, "WritePeaksToTextFile", PeaksAreStored);
}
private PeakFitType GetDeconPeakFitType(Globals.PeakFitType peakFitType)
{
switch (peakFitType)
{
case Globals.PeakFitType.Undefined:
throw new Exception("Failed to convert PeakType to DeconEnginePeakType");
case Globals.PeakFitType.APEX:
return(Deconvoluters.HornDeconvolutor.ThrashV1.PeakProcessing.PeakFitType.Apex);
case Globals.PeakFitType.LORENTZIAN:
return(Deconvoluters.HornDeconvolutor.ThrashV1.PeakProcessing.PeakFitType.Lorentzian);
case Globals.PeakFitType.QUADRATIC:
return(Deconvoluters.HornDeconvolutor.ThrashV1.PeakProcessing.PeakFitType.Quadratic);
default:
return(Deconvoluters.HornDeconvolutor.ThrashV1.PeakProcessing.PeakFitType.Apex);
}
}
