TransformationModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: $
// $Authors: Hendrik Weisser $
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#ifndef OPENMS_ANALYSIS_MAPMATCHING_TRANSFORMATIONMODEL_H
#define OPENMS_ANALYSIS_MAPMATCHING_TRANSFORMATIONMODEL_H

#include <OpenMS/DATASTRUCTURES/Param.h>

#include <gsl/gsl_bspline.h>
#include <gsl/gsl_interp.h>

namespace OpenMS
{
  class OPENMS_DLLAPI TransformationModel
  {
public:
    typedef std::pair<DoubleReal, DoubleReal> DataPoint;
    typedef std::vector<DataPoint> DataPoints;

    TransformationModel() {}

    TransformationModel(const TransformationModel::DataPoints &,
                        const Param &) :
      params_() {}

    virtual ~TransformationModel() {}

    virtual DoubleReal evaluate(const DoubleReal value) const
    {
      return value;
    }

    void getParameters(Param & params) const
    {
      params = params_;
    }

    static void getDefaultParameters(Param & params)
    {
      params.clear();
    }

protected:
    Param params_;
  };


  class OPENMS_DLLAPI TransformationModelLinear :
    public TransformationModel
  {
public:
    TransformationModelLinear(const DataPoints & data, const Param & params);

    ~TransformationModelLinear();

    virtual DoubleReal evaluate(const DoubleReal value) const;

    using TransformationModel::getParameters;

    void getParameters(DoubleReal & slope, DoubleReal & intercept) const;

    static void getDefaultParameters(Param & params);

    void invert();

protected:
    DoubleReal slope_, intercept_;
    bool data_given_;
    bool symmetric_;
  };


  class OPENMS_DLLAPI TransformationModelInterpolated :
    public TransformationModel
  {
public:
    TransformationModelInterpolated(const DataPoints & data,
                                    const Param & params);

    ~TransformationModelInterpolated();

    DoubleReal evaluate(const DoubleReal value) const;

    static void getDefaultParameters(Param & params);

protected:
    std::vector<double> x_, y_;
    size_t size_;
    gsl_interp_accel * acc_;
    gsl_interp * interp_;
    TransformationModelLinear * lm_;
  };


  class OPENMS_DLLAPI TransformationModelBSpline :
    public TransformationModel
  {
public:
    TransformationModelBSpline(const DataPoints & data, const Param & params);

    ~TransformationModelBSpline();

    DoubleReal evaluate(const DoubleReal value) const;

    static void getDefaultParameters(Param & params);

protected:
    void getQuantiles_(const gsl_vector * x, const std::vector<double> &
                       quantiles, gsl_vector * results);

    void computeFit_();

    void computeLinear_(const double pos, double & slope, double & offset,
                        double & sd_err);

    gsl_vector * x_, * y_, * w_, * bsplines_, * coeffs_;
    gsl_matrix * cov_;
    gsl_bspline_workspace * workspace_;
    size_t size_, ncoeffs_;
    // First/last breakpoint
    double xmin_, xmax_;
    double slope_min_, slope_max_, offset_min_, offset_max_;
    double sd_err_left_, sd_err_right_;
  };

} // end of namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_TRANSFORMATIONMODEL_H