AbstractCodonFrequenciesSubstitutionModel.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AbstractCodonFrequenciesSubstitutionModel.h"
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
AbstractCodonFrequenciesSubstitutionModel::AbstractCodonFrequenciesSubstitutionModel(
    unique_ptr<CodonFrequencySetInterface> pfreq,
    const string& prefix) :
  AbstractParameterAliasable(prefix),
  pfreqset_(std::move(pfreq)),
  freqName_("")
{
  freqName_ = pfreqset_->getNamespace();
  pfreqset_->setNamespace(prefix + freqName_);
  addParameters_(pfreqset_->getParameters());
}
 
/******************************************************************************/
 
AbstractCodonFrequenciesSubstitutionModel::~AbstractCodonFrequenciesSubstitutionModel() {}
 
/******************************************************************************/
 
void AbstractCodonFrequenciesSubstitutionModel::fireParameterChanged(const ParameterList& parameters)
{
  pfreqset_->matchParametersValues(parameters);
}
 
/******************************************************************************/
 
void AbstractCodonFrequenciesSubstitutionModel::setFreq(map<int, double>& frequencies)
{
  pfreqset_->setFrequenciesFromAlphabetStatesFrequencies(frequencies);
  matchParametersValues(pfreqset_->getParameters());
}
 
/******************************************************************************/
 
double AbstractCodonFrequenciesSubstitutionModel::getCodonsMulRate(size_t i, size_t j) const
{
  return pfreqset_->getFrequencies()[j];
}
 
/******************************************************************************/