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// $Maintainer: Timo Sachsenberg $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MAXLIKELIFITTER1D_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MAXLIKELIFITTER1D_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>

namespace OpenMS
{

  /**
  @brief Abstract base class for all 1D-model fitters using maximum likelihood optimization.
  */
  class OPENMS_DLLAPI MaxLikeliFitter1D :
    public Fitter1D
  {

public:

    /// default constructor
    MaxLikeliFitter1D() :
      Fitter1D()
    {
    }

    /// copy constructor
    MaxLikeliFitter1D(const MaxLikeliFitter1D & source) :
      Fitter1D(source)
    {
    }

    /// destructor
    virtual ~MaxLikeliFitter1D()
    {
    }

    /// assignment operator
    virtual MaxLikeliFitter1D & operator=(const MaxLikeliFitter1D & source)
    {
      if (&source == this) return *this;

      Fitter1D::operator=(source);

      return *this;
    }

protected:

    /// fit an offset on the basis of the Pearson correlation coefficient
    QualityType fitOffset_(InterpolationModel * model, const RawDataArrayType & set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step)
    {
      const CoordinateType offset_min = model->getInterpolation().supportMin() - stdev1;
      const CoordinateType offset_max = model->getInterpolation().supportMin() + stdev2;

      CoordinateType offset;
      QualityType correlation;

      //test model with default offset
      std::vector<float> real_data;
      real_data.reserve(set.size());
      std::vector<float> model_data;
      model_data.reserve(set.size());

      for (Size i = 0; i < set.size(); ++i)
      {
        real_data.push_back(set[i].getIntensity());
        model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
      }

      CoordinateType max_offset = model->getInterpolation().getOffset();
      QualityType max_correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());

      //test different offsets
      for (offset = offset_min; offset <= offset_max; offset += offset_step)
      {
        // set offset
        model->setOffset(offset);

        // get samples
        model_data.clear();
        for (Size i = 0; i < set.size(); ++i)
        {
          model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
        }

        correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());

        if (correlation > max_correlation)
        {
          max_correlation = correlation;
          max_offset = offset;
        }
      }

      model->setOffset(max_offset);

      return max_correlation;
    }

    void updateMembers_()
    {
      Fitter1D::updateMembers_();
    }

  };
}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_MAXLIKELIFITTER1D_H
