EGHTraceFitter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
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#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/TraceFitter.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI EGHTraceFitter :
    public TraceFitter
  {
public:
    class EGHTraceFunctor :
      public TraceFitter::GenericFunctor
    {
public:
 
      EGHTraceFunctor(int dimensions,
                      const TraceFitter::ModelData* data);
 
      ~EGHTraceFunctor() override;
 
      int operator()(const Eigen::VectorXd& x, Eigen::VectorXd& fvec) override;
 
      // compute Jacobian matrix for the different parameters
      int df(const Eigen::VectorXd& x, Eigen::MatrixXd& J) override;
 
protected:
      const TraceFitter::ModelData* m_data;
    };
 
    EGHTraceFitter();
 
    EGHTraceFitter(const EGHTraceFitter& other);
 
    EGHTraceFitter& operator=(const EGHTraceFitter& source);
 
    ~EGHTraceFitter() override;
 
    // override important methods
    void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces) override;
 
    double getLowerRTBound() const override;
 
    double getTau() const;
 
    double getUpperRTBound() const override;
 
    double getHeight() const override;
 
    double getSigma() const;
 
    double getCenter() const override;
 
    bool checkMaximalRTSpan(const double max_rt_span) override;
 
    bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span) override;
 
    double getValue(double rt) const override;
 
    double getArea() override;
 
    double getFWHM() const override;
 
    String getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift) override;
 
protected:
    double apex_rt_;
    double height_;
 
    double sigma_;
    double tau_;
 
    std::pair<double, double> sigma_5_bound_;
 
    double region_rt_span_;
 
    static const double EPSILON_COEFS_[];
 
    static const Size NUM_PARAMS_;
 
    std::pair<double, double> getAlphaBoundaries_(const double alpha) const;
 
    void getOptimizedParameters_(const Eigen::VectorXd& x_init) override;
 
    void setInitialParameters_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces);
 
    void updateMembers_() override;
  };
 
} // namespace OpenMS