AbstractCodonAARateSubstitutionModel.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/NumConstants.h>
 
#include "AbstractCodonAARateSubstitutionModel.h"
 
using namespace bpp;
 
using namespace std;
 
/******************************************************************************/
 
AbstractCodonAARateSubstitutionModel::AbstractCodonAARateSubstitutionModel(
    std::shared_ptr<ProteinSubstitutionModelInterface> pmodel,
    std::shared_ptr<const GeneticCode> pgencode,
    const string& prefix,
    bool paramSynRate) :
  AbstractParameterAliasable(prefix),
  pAAmodel_(pmodel),
  pgencode_(pgencode),
  beta_(19),
  gamma_(1),
  stateMap_(new CanonicalStateMap(pgencode->getSourceAlphabet(), false))
{
  if (paramSynRate)
    addParameter_(new Parameter(prefix + "gamma", 1, std::make_shared<IntervalConstraint>(NumConstants::SMALL(), 999, true, true)));
 
  addParameter_(new Parameter(prefix + "beta", 1, Parameter::R_PLUS_STAR));
 
  pAAmodel_->enableEigenDecomposition(false);
 
  pAAmodel_->setNamespace(prefix + pAAmodel_->getNamespace());
  addParameters_(pAAmodel_->getParameters());
}
 
void AbstractCodonAARateSubstitutionModel::fireParameterChanged(const ParameterList& parameters)
{
  pAAmodel_->matchParametersValues(parameters);
 
  if (hasParameter("gamma"))
    gamma_ = getParameterValue("gamma");
 
  beta_ = getParameterValue("beta");
}
 
double AbstractCodonAARateSubstitutionModel::getCodonsMulRate(size_t i, size_t j) const
{
  int si(stateMap_->getAlphabetStateAsInt(i)), sj(stateMap_->getAlphabetStateAsInt(j));
 
  return pgencode_->areSynonymous(si, sj) ? gamma_ :
         beta_* pAAmodel_->Qij(pAAmodel_->getModelStates(pgencode_->translate(si))[0],
        pAAmodel_->getModelStates(pgencode_->translate(sj))[0]);
}