D1WalkSubstitutionModel.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "D1WalkSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Container/SequenceContainerTools.h>
 
using namespace bpp;
 
#include <cmath>
#include <map>
 
using namespace std;
 
/******************************************************************************/
 
D1WalkSubstitutionModel::D1WalkSubstitutionModel(std::shared_ptr<const IntegerAlphabet> alpha, unsigned short method) :
  AbstractParameterAliasable("D1Walk."),
  AbstractReversibleSubstitutionModel(alpha, std::shared_ptr<StateMapInterface>(new CanonicalStateMap(alpha, false)), "D1Walk."),
  freqSet_(0)
{
  freqSet_ = std::make_shared<FullFrequencySet>(getStateMap(), true, method);
  freqSet_->setNamespace("D1Walk.");
  computeFrequencies(false);
 
  addParameters_(freqSet_->getParameters());
  // Exchangeability Matrix:
  for (unsigned int i = 0; i < size_ - 1; i++)
  {
    exchangeability_(i, i + 1) = 1;
  }
 
  for (unsigned int i = 1; i < size_; i++)
  {
    exchangeability_(i, i - 1) = 1;
  }
 
  updateMatrices_();
}
 
/******************************************************************************/
 
void D1WalkSubstitutionModel::updateMatrices_()
{
  // Frequencies:
  freq_ = freqSet_->getFrequencies();
 
  AbstractReversibleSubstitutionModel::updateMatrices_();
}
 
 
/******************************************************************************/
 
void D1WalkSubstitutionModel::setFreq(std::map<int, double>& freqs)
{
  for (auto i : freqs)
  {
    freq_[(size_t)i.first] = i.second;
  }
 
  freqSet_->setFrequencies(freq_);
  // Update parameters and re-compute generator and eigen values:
  matchParametersValues(freqSet_->getParameters());
}
 
/******************************************************************************/