AutoCorrelationSequenceEvolution.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AutoCorrelationSequenceEvolution.h"
 
using namespace std;
using namespace bpp;
 
/******************************************************************************/
 
AutoCorrelationSequenceEvolution::AutoCorrelationSequenceEvolution(
    std::shared_ptr<SubstitutionProcessCollection> processColl,
    std::vector<size_t>& nProc) :
  MultiProcessSequenceEvolution(processColl, nProc),
  hmmAlph_(),
  autoCorrTransMat_()
{
  hmmAlph_ = make_unique<HmmProcessAlphabet>(processColl_, nProc);
 
  autoCorrTransMat_ = make_unique<AutoCorrelationTransitionMatrix>(hmmAlph_, "AutoCorr.");
 
  // initialize parameters:
  addParameters_(hmmAlph_->getParameters());
  addParameters_(autoCorrTransMat_->getParameters());
}
 
 
void AutoCorrelationSequenceEvolution::setNamespace(const std::string& nameSpace)
{
  deleteParameters_(hmmAlph_->getParameters().getParameterNames());
  deleteParameters_(autoCorrTransMat_->getParameters().getParameterNames());
 
  hmmAlph_->setNamespace(nameSpace);
  autoCorrTransMat_->setNamespace(nameSpace);
 
  addParameters_(hmmAlph_->getParameters());
  addParameters_(autoCorrTransMat_->getParameters());
}
 
 
void AutoCorrelationSequenceEvolution::fireParameterChanged(const ParameterList& parameters)
{
  MultiProcessSequenceEvolution::fireParameterChanged(parameters);
 
  hmmAlph_->matchParametersValues(parameters);
  autoCorrTransMat_->matchParametersValues(parameters);
}
 
ParameterList AutoCorrelationSequenceEvolution::getNonDerivableParameters() const
{
  ParameterList pl = MultiProcessSequenceEvolution::getNonDerivableParameters();
 
  pl.includeParameters(autoCorrTransMat_->getParameters());
 
  return pl;
}