GaussTraceFitter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Marc Sturm$
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_GAUSSTRACEFITTER_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_GAUSSTRACEFITTER_H

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

namespace OpenMS
{

  class OPENMS_DLLAPI GaussTraceFitter :
    public TraceFitter
  {
public:
    GaussTraceFitter();

    GaussTraceFitter(const GaussTraceFitter& other);

    GaussTraceFitter& operator=(const GaussTraceFitter& source);

    virtual ~GaussTraceFitter();

    // override important methods
    void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);

    double getLowerRTBound() const;

    double getUpperRTBound() const;

    double getHeight() const;

    double getCenter() const;

    double getFWHM() const;

    double getSigma() const;

    bool checkMaximalRTSpan(const double max_rt_span);

    bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span);

    double getValue(double rt) const;

    double getArea();

    String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift);

protected:
    double sigma_;
    double x0_;
    double height_;
    double region_rt_span_;

    static const Size NUM_PARAMS_;

    void getOptimizedParameters_(const Eigen::VectorXd& x_init);

    class GaussTraceFunctor :
      public TraceFitter::GenericFunctor
    {
public:
      GaussTraceFunctor(int dimensions,
                        const TraceFitter::ModelData* data);

      int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec);

      // compute Jacobian matrix for the different parameters
      int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J);
protected:
      const TraceFitter::ModelData* m_data;
    };

    void setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);

    virtual void updateMembers_();

  };

} // namespace OpenMS

#endif // #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKEDTRACEFITTERGAUSS_H