AbstractBiblioSubstitutionModel.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AbstractBiblioSubstitutionModel.h"
 
using namespace bpp;
using namespace std;
 
AbstractBiblioTransitionModel::AbstractBiblioTransitionModel(const std::string& prefix) :
  // AbstractParameterAliasable(prefix),
  mapParNamesFromPmodel_(),
  lParPmodel_()
{}
 
/******************************************************************************/
 
AbstractBiblioTransitionModel::AbstractBiblioTransitionModel(const AbstractBiblioTransitionModel& model) :
  // AbstractParameterAliasable(model),
  mapParNamesFromPmodel_(model.mapParNamesFromPmodel_),
  lParPmodel_(model.lParPmodel_)
{}
 
/******************************************************************************/
 
AbstractBiblioTransitionModel& AbstractBiblioTransitionModel::operator=(const AbstractBiblioTransitionModel& model)
{
  AbstractParameterAliasable::operator=(model);
  mapParNamesFromPmodel_ = model.mapParNamesFromPmodel_;
  lParPmodel_            = model.lParPmodel_;
  return *this;
}
 
 
/******************************************************************************/
 
std::string AbstractBiblioTransitionModel::getParNameFromPmodel(const std::string& name) const
{
  auto it = mapParNamesFromPmodel_.find(name);
  if (it == mapParNamesFromPmodel_.end())
    throw Exception("AbstractBiblioTransitionModel::getParNameFromPmodel : unknown parameter " + name);
  return it->second;
}
 
/******************************************************************************/
 
std::string AbstractBiblioTransitionModel::getPmodelParName(const std::string& name) const
{
  for (auto it : mapParNamesFromPmodel_)
  {
    if (it.second == name)
      return it.first;
  }
 
  throw Exception("AbstractBiblioTransitionModel::getPmodelParName: unknown parameter name " + name);
}
 
 
/******************************************************************************/
 
void AbstractBiblioTransitionModel::updateMatrices_()
{
  for (size_t i = 0; i < lParPmodel_.size(); ++i)
  {
    if (mapParNamesFromPmodel_.find(lParPmodel_[i].getName()) != mapParNamesFromPmodel_.end())
    {
      lParPmodel_[i].setValue(parameter(getParameterNameWithoutNamespace(mapParNamesFromPmodel_[lParPmodel_[i].getName()])).getValue());
    }
  }
 
  model_().matchParametersValues(lParPmodel_);
}
 
/******************************************************************************/
 
void AbstractBiblioTransitionModel::addRateParameter()
{
  model_().addRateParameter();
  addParameter_(new Parameter(getNamespace() + "rate", model().getRate(), Parameter::R_PLUS_STAR));
 
  mapParNamesFromPmodel_[getNamespace() + "rate"] = "rate";
  lParPmodel_.reset();
  lParPmodel_.addParameters(model().getParameters());
}
 
/******************************************************************************/
 
void AbstractBiblioTransitionModel::setNamespace(const string& name)
{
  AbstractParameterAliasable::setNamespace(name);
 
  map<string, string> mapParNamesFromPmodel_new;
 
  for (const auto& it : mapParNamesFromPmodel_)
  {
    mapParNamesFromPmodel_new[name + model().getParameterNameWithoutNamespace(it.first)] = it.second;
  }
 
  mapParNamesFromPmodel_.clear();
  mapParNamesFromPmodel_ = mapParNamesFromPmodel_new;
 
  model_().setNamespace(name);
 
  lParPmodel_.reset();
  lParPmodel_.addParameters(model().getParameters());
}
 
 
/******************************************************************************/
 
void AbstractBiblioTransitionModel::setFreq(std::map<int, double>& frequ)
{
  AbstractTotallyWrappedTransitionModel::setFreq(frequ);
 
  ParameterList pl;
  for (const auto& it : mapParNamesFromPmodel_)
  {
    pl.addParameter(Parameter(getNamespace() + it.second, model().getParameterValue(model().getParameterNameWithoutNamespace(it.first))));
  }
 
  matchParametersValues(pl);
}
 
 
void AbstractBiblioTransitionModel::setFreqFromData(
    const SequenceDataInterface& data, double pseudoCount)
{
  map<int, double> freqs;
  SequenceContainerTools::getFrequencies(data, freqs, pseudoCount);
  setFreq(freqs);
}