KCM.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/NumConstants.h>
 
#include "../FrequencySet/CodonFrequencySet.h"
#include "../Nucleotide/GTR.h"
#include "KCM.h"
 
using namespace bpp;
 
using namespace std;
 
/******************************************************************************/
 
KCM::KCM(
    std::shared_ptr<const GeneticCode> gc,
    bool oneModel) :
  AbstractParameterAliasable("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractWrappedModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractWrappedTransitionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractTotallyWrappedTransitionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractBiblioTransitionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractWrappedSubstitutionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractTotallyWrappedSubstitutionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  AbstractBiblioSubstitutionModel("KCM" + string(oneModel ? "7" : "19") + "."),
  pmodel_(),
  oneModel_(oneModel)
{
  shared_ptr<const NucleicAlphabet> nalph = gc->codonAlphabet().getNucleicAlphabet();
 
  if (oneModel)
    pmodel_.reset(new KroneckerCodonDistanceSubstitutionModel(
          gc,
          make_unique<GTR>(nalph)));
  else
    pmodel_.reset(new KroneckerCodonDistanceSubstitutionModel(
          gc,
          make_unique<GTR>(nalph),
          make_unique<GTR>(nalph),
          make_unique<GTR>(nalph)));
 
  string name = "KCM" + string(oneModel ? "7" : "19") + ".";
 
  pmodel_->setNamespace(name);
 
  addParameters_(pmodel_->getParameters());
 
  getParameter_("beta").setName(name + "omega"),
 
  lParPmodel_.addParameters(pmodel_->getParameters());
 
  vector<std::string> v = lParPmodel_.getParameterNames();
 
  for (auto& vi : v)
  {
    mapParNamesFromPmodel_[vi] = getParameterNameWithoutNamespace(vi);
  }
 
  mapParNamesFromPmodel_[name + "beta"] = "omega";
 
  updateMatrices_();
}
 
 
KCM::KCM(const KCM& kcm) :
  AbstractParameterAliasable(kcm),
  AbstractWrappedModel(kcm),
  AbstractWrappedTransitionModel(kcm),
  AbstractTotallyWrappedTransitionModel(kcm),
  AbstractBiblioTransitionModel(kcm),
  AbstractWrappedSubstitutionModel(kcm),
  AbstractTotallyWrappedSubstitutionModel(kcm),
  AbstractBiblioSubstitutionModel(kcm),
  pmodel_(new KroneckerCodonDistanceSubstitutionModel(*kcm.pmodel_)),
  oneModel_(kcm.oneModel_)
{}
 
KCM& KCM::operator=(const KCM& kcm)
{
  AbstractBiblioSubstitutionModel::operator=(kcm);
 
  oneModel_ = kcm.oneModel_;
  pmodel_.reset(new KroneckerCodonDistanceSubstitutionModel(*kcm.pmodel_));
  return *this;
}