//
// File: CodonDistanceSubstitutionModel.h
// Created by: Laurent Gueguen
// Created on: Tue Dec 24 11:03:53 2003
//

/*
  Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)

  This software is a computer program whose purpose is to provide classes
  for phylogenetic data analysis.

  This software is governed by the CeCILL  license under French law and
  abiding by the rules of distribution of free software.  You can  use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".

  As a counterpart to the access to the source code and  rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty  and the software's author,  the holder of the
  economic rights,  and the successive licensors  have only  limited
  liability.

  In this respect, the user's attention is drawn to the risks associated
  with loading,  using,  modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean  that it is complicated to manipulate,  and  that  also
  therefore means  that it is reserved for developers  and  experienced
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards their
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  same conditions as regards security.

  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _CODONDISTANCESUBSTITUTIONMODEL_H_
#define _CODONDISTANCESUBSTITUTIONMODEL_H_

#include "AbstractCodonDistanceSubstitutionModel.h"
#include "AbstractCodonSubstitutionModel.h"

namespace bpp
{
  /**
   * @brief Class for substitution models of codons with
   * non-synonymous/synonymous ratios of substitution rates defined
   * through a distance between amino-acids.
   *
   * @author Laurent Guéguen
   *
   * Objects of this class are built from three substitution models of
   * NucleicAlphabets. No model is directly accessible. </p>
   *
   * Only substitutions with one letter changed are accepted. </p>
   *
   * If a distance @f$d@f$ between amino-acids is defined, the ratio between
   * non-synonymous and synonymous substitutions rates is, if the codied
   * amino-acids are @f$x@f$ and @f$y@f$, @f$\beta*\exp(-\alpha.d(x,y))@f$ with
   * non-negative parameter \c "alpha" and positive parameter \c "beta".
   *
   * If such a distance is not defined, the ratio between non-synonymous
   * and synonymous substitutions rates is @f$\beta@f$ with positive
   * parameter \c "beta".
   *
   */

  class CodonDistanceSubstitutionModel :
    public AbstractCodonSubstitutionModel,
    public AbstractCodonDistanceSubstitutionModel
  {
  public:
    /**
     * @brief Build a new CodonDistanceSubstitutionModel object from
     * a pointer to NucleotideSubstitutionModel.
     *
     * @param gCode pointer to a GeneticCode
     * @param pmod  pointer to the NucleotideSubstitutionModel to use in the three positions.
     * The instance will then own this substitution model.
     * @param pdist optional pointer to a distance between amino-acids
     */
    CodonDistanceSubstitutionModel(
        const GeneticCode* gCode,
        NucleotideSubstitutionModel* pmod,
        const AlphabetIndex2* pdist);

    /**
     * @brief Build a new CodonDistanceSubstitutionModel object
     * from three pointers to NucleotideSubstitutionModels.
     *
     * @param gCode pointer to a GeneticCode
     * @param pmod1, pmod2, pmod3 pointers to the
     *   NucleotideSubstitutionModels to use in the three positions.
     *   Either all the models are different objects to avoid parameters
     *   redondancy, or only the first model is used in every position.
     *   The used models are owned by the instance.
     * @param pdist optional pointer to the AlphabetIndex2 amino-acids distance object.
     */
    CodonDistanceSubstitutionModel(
        const GeneticCode* gCode,
        NucleotideSubstitutionModel* pmod1,
        NucleotideSubstitutionModel* pmod2,
        NucleotideSubstitutionModel* pmod3,
        const AlphabetIndex2* pdist);

    virtual ~CodonDistanceSubstitutionModel() {}

    CodonDistanceSubstitutionModel* clone() const
    {
      return new CodonDistanceSubstitutionModel(*this);
    }

  public:
    void fireParameterChanged(const ParameterList& parameterlist);
  
    std::string getName() const;

    double getCodonsMulRate(size_t i, size_t j) const;
  };
} // end of namespace bpp.

#endif //_CODONDISTANCESUBSTITUTIONMODEL_H_

