//
// File: LG08.h
// Created by: Laurent Gueguen
// Created on: Wed lundi 13 septembre 2010, à 13h 26
//

/*
  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
  requirements in conditions enabling the security of their systems and/or 
  data to be ensured and,  more generally, to use and operate it in the 
  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 _LG08_H_
#define _LG08_H_

#include "ProteinSubstitutionModel.h"
#include "../AbstractSubstitutionModel.h"
#include "../FrequenciesSet/ProteinFrequenciesSet.h"

// From SeqLib:
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>

namespace bpp
{

  /**
   * @brief The Le and Gascuel substitution model for proteins.
   *
   * The exchangability matrix is normalized so that \f$Q = S . \pi\f$ and \f$\sum_i Q_{i,i}\pi_i = -1\f$.
   * The original frequencies can be used, or alternatively a parametrized version, corresponding to the
   * so-called LG08+F model.
   * Eigen values and vectors are obtained numerically.
   * 
   * Reference:
   * - Le, Si Q. and Gascuel, O. (2008), _Molecular Biology And Evolution_ 25, 1307--1320. 
   */
  class LG08 :
    public virtual ProteinSubstitutionModel,
    public AbstractReversibleSubstitutionModel
  {
  private:
    ProteinFrequenciesSet* freqSet_;

  public:
    /**
     * @brief Build a simple LG08 model, with original equilibrium frequencies.
     *
     * @param alpha A proteic alphabet.
     */
    LG08(const ProteicAlphabet* alpha);

    /**
     * @brief Build a LG08 model with special equilibrium frequencies.
     *
     * @param alpha A proteic alphabet.
     * @param freqSet A pointer toward a protein frequencies set, which will be owned by this instance.
     * @param initFreqs Tell if the frequency set should be initialized with the original LG08 values.
     * Otherwise, the values of the set will be used.
     */
    LG08(const ProteicAlphabet* alpha, ProteinFrequenciesSet* freqSet, bool initFreqs=false);

    LG08(const LG08& model) :
      AbstractParameterAliasable(model),
      //AbstractSubstitutionModel(model),
      AbstractReversibleSubstitutionModel(model),
      freqSet_(dynamic_cast<ProteinFrequenciesSet*>(model.freqSet_->clone()))
    {}

    LG08& operator=(const LG08& model)
    {
      AbstractParameterAliasable::operator=(model);
      AbstractSubstitutionModel::operator=(model);
      AbstractReversibleSubstitutionModel::operator=(model);
      if (freqSet_) delete freqSet_;
      freqSet_ = dynamic_cast<ProteinFrequenciesSet*>(model.freqSet_->clone());
      return *this;
    }

    virtual ~LG08() { delete freqSet_; }

#ifndef NO_VIRTUAL_COV
    LG08*
#else
    Clonable*
#endif
    clone() const { return new LG08(*this); }

  public:
    std::string getName() const 
    { 
      if (freqSet_->getNamespace().find("LG08+F.")!=std::string::npos)
        return "LG08+F"; 
      else 
        return "LG08"; 
    }

    void fireParameterChanged(const ParameterList& parameters)
    {
      freqSet_->matchParametersValues(parameters);
      freq_ = freqSet_->getFrequencies();
      AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
    }

    void setFrequenciesSet(const ProteinFrequenciesSet& freqSet)
    {
      delete freqSet_;
      freqSet_ = dynamic_cast<ProteinFrequenciesSet*>(freqSet.clone());
      resetParameters_();
      addParameters_(freqSet_->getParameters());
    }

    const FrequenciesSet* getFrequenciesSet() const { return freqSet_; }

    void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0);

  };

} //end of namespace bpp.

#endif	//_LG08_H_

