TripletSubstitutionModel.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/Matrix/EigenValue.h>
#include <Bpp/Numeric/Matrix/MatrixTools.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "TripletSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/WordAlphabet.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>
 
using namespace bpp;
 
// From the STL:
#include <cmath>
 
using namespace std;
 
/******************************************************************************/
 
TripletSubstitutionModel::TripletSubstitutionModel(
    std::shared_ptr<const CodonAlphabet> palph,
    std::unique_ptr<NucleotideSubstitutionModelInterface> pmod) :
  AbstractParameterAliasable("Triplet."),
  WordSubstitutionModel(palph, make_shared<CanonicalStateMap>(palph, false), "Triplet.")
{
  unsigned int i;
  addParameters_(pmod->getParameters());
 
  Vrate_.resize(3);
  for (i = 0; i < 3; i++)
  {
    VSubMod_.push_back(std::move(pmod));
    VnestedPrefix_.push_back(VSubMod_[i]->getNamespace());
    Vrate_[i] = 1. / 3.;
  }
 
  // relative rates
  for (i = 0; i < 2; i++)
  {
    addParameter_(new Parameter("Triplet.relrate" + TextTools::toString(i + 1), 1.0 / (3 - i), Parameter::PROP_CONSTRAINT_EX));
  }
 
  WordSubstitutionModel::updateMatrices_();
}
 
TripletSubstitutionModel::TripletSubstitutionModel(
    std::shared_ptr<const CodonAlphabet> palph,
    std::unique_ptr<NucleotideSubstitutionModelInterface> pmod1,
    std::unique_ptr<NucleotideSubstitutionModelInterface> pmod2,
    std::unique_ptr<NucleotideSubstitutionModelInterface> pmod3) :
  AbstractParameterAliasable("Triplet."),
  WordSubstitutionModel(palph, make_shared<CanonicalStateMap>(palph, false), "Triplet.")
{
  string st = "Triplet.";
 
  VSubMod_.push_back(std::move(pmod1));
  VnestedPrefix_.push_back(VSubMod_[0]->getNamespace());
  VSubMod_[0]->setNamespace(st + "1_" + VnestedPrefix_[0]);
  addParameters_(VSubMod_[0]->getParameters());
 
  VSubMod_.push_back(std::move(pmod2));
  VnestedPrefix_.push_back(VSubMod_[1]->getNamespace());
  VSubMod_[1]->setNamespace(st + "2_" + VnestedPrefix_[1]);
  addParameters_(VSubMod_[1]->getParameters());
 
  VSubMod_.push_back(std::move(pmod3));
  VnestedPrefix_.push_back(VSubMod_[2]->getNamespace());
  VSubMod_[2]->setNamespace(st + "3_" + VnestedPrefix_[2]);
  addParameters_(VSubMod_[2]->getParameters());
 
  Vrate_.resize(3);
  for (unsigned int i = 0; i < 3; ++i)
  {
    Vrate_[i] = 1.0 / 3;
  }
 
  // relative rates
  for (unsigned int i = 0; i < 2; ++i)
  {
    addParameter_(new Parameter(st + "relrate" + TextTools::toString(i + 1), 1.0 / (3 - i), Parameter::PROP_CONSTRAINT_EX));
  }
 
  WordSubstitutionModel::updateMatrices_();
}
 
string TripletSubstitutionModel::getName() const
{
  string s = "TripletSubstitutionModel model:";
  for (auto& vi :  VSubMod_)
  {
    s += " " + vi->getName();
  }
 
  return s;
}