LmaIsotopeFitter1D.h

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// $Maintainer: Clemens Groepl $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAISOTOPEFITTER1D_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAISOTOPEFITTER1D_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>



namespace OpenMS
{
  class OPENMS_DLLAPI LmaIsotopeFitter1D :
    public LevMarqFitter1D
  {
public:

    enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};

    LmaIsotopeFitter1D();

    LmaIsotopeFitter1D(const LmaIsotopeFitter1D & source);

    virtual ~LmaIsotopeFitter1D();

    virtual LmaIsotopeFitter1D & operator=(const LmaIsotopeFitter1D & source);

    static Fitter1D * create()
    {
      return new LmaIsotopeFitter1D();
    }

    static const String getProductName()
    {
      return "LmaIsotopeFitter1D";
    }

    QualityType fit1d(const RawDataArrayType & range, InterpolationModel * & model);

protected:

    struct Data
    {
      typedef Peak1D PeakType;
      typedef std::vector<PeakType> RawDataArrayType;
      typedef std::vector<double> ContainerType;
      typedef Feature::CoordinateType CoordinateType;

      Size n;
      RawDataArrayType set;
      ContainerType isotopes_exact;
      CoordinateType isotope_distance;
      // bool mono_known;
      // CoordinateType monoisotopic_mz;
      CoordinateType isotopes_stdev;
      CoordinateType sigma;
    };

    void setInitialParameters_();

    static Int residual_(const gsl_vector * x, void * params, gsl_vector * f);

    static Int jacobian_(const gsl_vector * x, void * params, gsl_matrix * J);

    static Int evaluate_(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J);

    void printState_(Int iter, gsl_multifit_fdfsolver * s);

    UInt charge_;
    CoordinateType isotope_stdev_;
    CoordinateType total_intensity_;
    CoordinateType monoisotopic_mz_;
    Int max_isotope_;
    DoubleReal trim_right_cutoff_;
    DoubleReal isotope_distance_;
    CoordinateType mean_;
    DoubleReal averagine_[AVERAGINE_NUM];
    ContainerType isotopes_exact_;
    bool monoisotopic_mass_known_;

    void updateMembers_();
  };
}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_LMAISOTOPEFITTER1D_H