AbstractMixedSubstitutionModel.h

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//
// File: MixedSubstitutionModel.h
// Created by: Laurent Gueguen
// On: vendredi 19 novembre 2010, à 15h 48
//

/*
   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
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   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 _ABSTRACTMIXEDSUBSTITUTIONMODEL_H_
#define _ABSTRACTMIXEDSUBSTITUTIONMODEL_H_

#include "MixedSubstitutionModel.h"
#include "AbstractSubstitutionModel.h"
// #include <Bpp/Seq/Alphabet.all>

#include <vector>
#include <string>
#include <map>
#include <cstring> // C lib for string copy

namespace bpp
{
class AbstractMixedSubstitutionModel :
  public virtual MixedSubstitutionModel,
  public AbstractSubstitutionModel
{
protected:
  std::vector<SubstitutionModel*> modelsContainer_;

  std::vector<double> vProbas_;

  std::vector<double> vRates_;

public:
  AbstractMixedSubstitutionModel(const Alphabet*, StateMap* stateMap, const std::string& prefix);

  AbstractMixedSubstitutionModel(const AbstractMixedSubstitutionModel&);

  AbstractMixedSubstitutionModel& operator=(const AbstractMixedSubstitutionModel&);

  virtual ~AbstractMixedSubstitutionModel();

  virtual AbstractMixedSubstitutionModel* clone() const = 0;

public:
  virtual size_t getNumberOfModels() const
  {
    return modelsContainer_.size();
  }

  virtual const SubstitutionModel* getNModel(size_t i) const
  {
    return modelsContainer_[i];
  }

  virtual SubstitutionModel* getNModel(size_t i)
  {
    return modelsContainer_[i];
  }

  double getNRate(size_t i) const
  {
    return vRates_[i];
  }

  virtual void setRate(double rate);

  virtual void setVRates(const Vdouble& vd);

  virtual void normalizeVRates();

  const std::vector<double>& getVRates() const
  {
    return vRates_;
  }

  virtual double getNProbability(size_t i) const
  {
    return vProbas_[i];
  }

  virtual const std::vector<double>& getProbabilities() const
  {
    return vProbas_;
  }

  virtual void setNProbability(size_t i, double prob)
  {
    if ((prob >= 0) && (prob <= 1))
      vProbas_[i] = prob;
  }

  double Qij(size_t i, size_t j) const {return 0; }

  virtual size_t getNumberOfStates() const;

  virtual const Matrix<double>& getPij_t(double t) const;
  virtual const Matrix<double>& getdPij_dt(double t) const;
  virtual const Matrix<double>& getd2Pij_dt2(double t) const;
};
} // end of namespace bpp.

#endif  // _ABSTRACTMIXEDSUBSTITUTIONMODEL_H_