libbpp-phyl-dev 2.2.0-1+b1 / usr / include / Bpp / Phyl / Model / Codon / YNGKP_M3.h

//
// File: YNGKP_M3.h
// Created by: Laurent Gueguen
// Created on: May 2010
//

/*
Copyright or © or Copr. CNRS, (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". 

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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
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In this respect, the user's attention is drawn to the risks associated
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that may mean  that it is complicated to manipulate,  and  that  also
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*/

#ifndef _YNGKP_M3_H_
#define _YNGKP_M3_H_

#include "../AbstractBiblioMixedSubstitutionModel.h"
#include "../MixtureOfASubstitutionModel.h"
#include "../FrequenciesSet/CodonFrequenciesSet.h"

#include <Bpp/Seq/GeneticCode/GeneticCode.h>

namespace bpp
{

/**
 * @brief The Yang et al (2000) M3 substitution model for codons.
 * @author Laurent Guéguen
 *
 * This model is a mixture of models as described in YN98 class, the
 * mixture being defined on the selection parameter to allow it to
 * vary among sites. There are $K$ selection parameters @f$ \omega_0 <
 * ... \omega_{K-1} @f$, with their respective probabilities @f$ p_0,
 * ..., p_{K-1} @f$ with @f$ p_0+p_1+...+p_{K-1}=1@f$. To garantee
 * that the @f$\omega_i@f$ are in increasing order, we define
 * @f$\delta_i=\omega_i - \omega_{i-1}@f$.
 *
 * This model includes 2*K parameters (@f$\kappa@f$, relative
 * probabilities @f$ theta1, theta2, ..., thetaK-1 @f$ and @f$omega0,
 * delta1, deltaK-1@f$). The codon frequencies @f$\pi_j@f$ are either
 * observed or infered.
 *
 * References:
 *
 * Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000)
 * Genetics 155:431-449.
 * 
 */
class YNGKP_M3:
    public AbstractBiblioMixedSubstitutionModel,
    virtual public ReversibleSubstitutionModel
{
private:
  std::auto_ptr<MixtureOfASubstitutionModel> pmixmodel_;

  /**
   * @brief indexes of 2 codons between which the substitution is
   * synonymous, to set a basis to the homogeneization of the rates.
   *
   */
  size_t synfrom_, synto_;
  
public:
  YNGKP_M3(const GeneticCode* gc, FrequenciesSet* codonFreqs, unsigned int nclass = 3);

  ~YNGKP_M3();
  
  YNGKP_M3* clone() const { return new YNGKP_M3(*this); }

  YNGKP_M3(const YNGKP_M3&);

  YNGKP_M3& operator=(const YNGKP_M3&);

protected:
  void updateMatrices();

public:
  const SubstitutionModel& getModel() const { return *pmixmodel_.get(); }

  const MixedSubstitutionModel& getMixedModel() const { return *pmixmodel_.get(); }

  std::string getName() const { return "YNGKP_M3"; }

private:
  SubstitutionModel& getModel() { return *pmixmodel_.get(); }
  
  MixedSubstitutionModel& getMixedModel() { return *pmixmodel_.get(); }
  
  const FrequenciesSet* getFrequenciesSet() const {return pmixmodel_->getNModel(1)->getFrequenciesSet();}

};

} //end of namespace bpp.

#endif	//_YNGKP_M3_H_