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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
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#pragma once

#include <OpenMS/DATASTRUCTURES/Matrix.h>

namespace OpenMS
{

  /**
      @brief Trained Local Linear %Map (LLM) model for peak intensity prediction

      This class offers a model for predictions of peptide peak heights
      (referred to as intensities) by a Local Linear %Map (LLM) model and
      is the basis of PeakIntensityPredictor.

      A general introduction to the Peak Intensity Predictor (PIP)
      can be found in the <A HREF="tutorial_pip.html">PIP Tutorial</A>.

      The model trained needs two files for storing the position of the
      codebook vectors and the linear mappings (codebooks.data, linearMapping.data)
      This is the default model used by PeakIntensityPredictor.
*/
  class OPENMS_DLLAPI LocalLinearMap
  {

public:

    /**
    @brief Define parameters needed by the Local Linear %Map (LLM) model

    Parameters xdim and ydim define the size of the two dimensional
    grid structure. Parameter radius gives the width of the Gaussian
    neighborhood function.
*/
    struct OPENMS_DLLAPI LLMParam
    {
      UInt xdim;           /**< size of first coordinate */
      UInt ydim;           /**< size of second coordinate */
      double radius;           /**< width of Gaussian neighborhood function */
    };

    /// default constructor
    LocalLinearMap();
    /// destructor
    virtual ~LocalLinearMap();

    ///return parameters of the LocalLinearMap model
    const LLMParam & getLLMParam() const;
    ///return position of the codebook vectors (18-dim)
    const Matrix<double> & getCodebooks() const;
    ///return linear mappings of the codebooks
    const Matrix<double> & getMatrixA() const;
    ///return linear bias
    const std::vector<double> & getVectorWout() const;
    ///return coordinates of codebook vectors on the 2-d grid
    const Matrix<UInt> & getCord() const;
    ///calculate and return normalized amino acid index variables from string representation of peptide
    void normalizeVector(std::vector<double> & aaIndexVariables);
    ///calculate neighborhood function based on distance of prototypes to winner prototype on two-dimensional grid structure and neighborhood width.
    std::vector<double> neigh(const Matrix<UInt> & cord, Size win, double radius);

private:

    LLMParam param_;                                            ///<parameters of the model
    Matrix<double> code_;                           ///<codebook vectors
    Matrix<double> A_;                              ///<linear mappings
    std::vector<double> wout_;              ///<linear bias
    Matrix<UInt> cord_;                                     ///<coordinates of codebooks on grid

    /// needed to store prototype coordinates
    Matrix<UInt> genCord_(Size xdim, Size ydim);
    ///calculate distance between two prototypes
    double dist_(const Matrix<UInt> & u, const Matrix<UInt> & v, Size a, Size b);

    ///Copy constructor not implemented => private
    LocalLinearMap(LocalLinearMap & rhs);
    ///Assignment operator not implemented => private
    LocalLinearMap & operator=(const LocalLinearMap & llm);

  };


}
