AutoCorrelationProcessPhyloLikelihood.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h>
 
#include "AutoCorrelationProcessPhyloLikelihood.h"
#include "HmmLikelihood_DF.h"
 
using namespace std;
using namespace bpp;
 
/******************************************************************************/
 
AutoCorrelationProcessPhyloLikelihood::AutoCorrelationProcessPhyloLikelihood(
    std::shared_ptr<const AlignmentDataInterface> data,
    std::shared_ptr<AutoCorrelationSequenceEvolution> processSeqEvol,
    std::shared_ptr<CollectionNodes> collNodes,
    size_t nSeqEvol,
    size_t nData) :
  AbstractPhyloLikelihood(collNodes->context()),
  AbstractAlignedPhyloLikelihood(collNodes->context(), data->getNumberOfSites()),
  AbstractSingleDataPhyloLikelihood(
      collNodes->context(),
      data->getNumberOfSites(),
      (processSeqEvol->getSubstitutionProcessNumbers().size() != 0)
          ? processSeqEvol->substitutionProcess(processSeqEvol->getSubstitutionProcessNumbers()[0]).getNumberOfStates()
    : 0,
      nData),
  AbstractSequencePhyloLikelihood(collNodes->context(), processSeqEvol, nData),
  AbstractParametrizable(""),
  MultiProcessSequencePhyloLikelihood(data, processSeqEvol, collNodes, nSeqEvol, nData),
  Hpep_(),
  hmm_()
{
  auto alphyl = make_shared<HmmPhyloAlphabet>(*this);
 
  Hpep_ = make_shared<HmmPhyloEmissionProbabilities>(alphyl);
 
  hmm_ = shared_ptr<HmmLikelihood_DF>(new HmmLikelihood_DF(context(), processSeqEvol->getHmmProcessAlphabet(), processSeqEvol->getHmmTransitionMatrix(), Hpep_));
 
  addParameters_(hmm_->getParameters());
}
 
void AutoCorrelationProcessPhyloLikelihood::setNamespace(const std::string& nameSpace)
{
  MultiProcessSequencePhyloLikelihood::setNamespace(nameSpace);
  hmm_->setNamespace(nameSpace);
}
 
 
void AutoCorrelationProcessPhyloLikelihood::fireParameterChanged(const ParameterList& parameters)
{
  MultiProcessSequencePhyloLikelihood::fireParameterChanged(parameters);
 
  hmm_->matchParametersValues(parameters);
}