KroneckerWordSubstitutionModel.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 "KroneckerWordSubstitutionModel.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;
 
/******************************************************************************/
 
KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(
    ModelList& modelList,
    const string& prefix) :
  AbstractParameterAliasable((prefix == "") ? "Kron." : prefix),
  AbstractKroneckerWordSubstitutionModel(
      modelList,
      (prefix == "") ? "Kron." : prefix)
{
  updateMatrices_();
}
 
KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(
    std::shared_ptr<const Alphabet> alph,
    std::shared_ptr<const StateMapInterface> stateMap,
    const string& prefix) :
  AbstractParameterAliasable((prefix == "") ? "Kron." : prefix),
  AbstractKroneckerWordSubstitutionModel(alph, stateMap, (prefix == "") ? "Kron." : prefix)
{
  enableEigenDecomposition(true);
}
 
KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(
    std::unique_ptr<SubstitutionModelInterface> pmodel,
    unsigned int num,
    const string& prefix) :
  AbstractParameterAliasable((prefix == "") ? "Kron." : prefix),
  AbstractKroneckerWordSubstitutionModel(std::move(pmodel),
      num,
      (prefix == "") ? "Kron." : prefix)
{
  enableEigenDecomposition(true);
  updateMatrices_();
}
 
KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(
    ModelList& modelList,
    const vector<set< size_t>>& vPos,
    const string& prefix) :
  AbstractParameterAliasable((prefix == "") ? "Kron." : prefix),
  AbstractKroneckerWordSubstitutionModel(
      modelList, vPos,
      (prefix == "") ? "Kron." : prefix)
{
  enableEigenDecomposition(true);
  updateMatrices_();
}
 
KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(
    std::unique_ptr<SubstitutionModelInterface> pmodel,
    unsigned int num,
    const vector<set< size_t>>& vPos,
    const string& prefix) :
  AbstractParameterAliasable((prefix == "") ? "Kron." : prefix),
  AbstractKroneckerWordSubstitutionModel(std::move(pmodel),
      num, vPos,
      (prefix == "") ? "Kron." : prefix)
{
  enableEigenDecomposition(true);
  updateMatrices_();
}
 
 
string KroneckerWordSubstitutionModel::getName() const
{
  return "Kron";
}