MvaFrequencySet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_FREQUENCYSET_MVAFREQUENCYSET_H
#define BPP_PHYL_MODEL_FREQUENCYSET_MVAFREQUENCYSET_H
 
 
#include "../Protein/Coala.h"
#include "ProteinFrequencySet.h"
 
namespace bpp
{
class MvaFrequencySet :
  public virtual ProteinFrequencySetInterface,
  public AbstractFrequencySet
{
public:
  MvaFrequencySet(std::shared_ptr<const ProteicAlphabet> alpha);
 
  MvaFrequencySet* clone() const override { return new MvaFrequencySet(*this); }
 
  /*
     MvaFrequencySet& operator=(const MvaFrequencySet& mfs)
     {
      AbstractFrequencySet::operator=(mfs);
      tPpalAxes_ = mfs.tPpalAxes_;
      rowCoords_ = mfs.rowCoords_;
      nbrOfAxes_ = mfs.nbrOfAxes_;
      model_ = mfs.model_;
      columnWeights_ = mfs.columnWeights_;
      paramValues_ = mfs.paramValues_;
      return *this;
     }
   */
 
protected:
  RowMatrix<double> tPpalAxes_;
  RowMatrix<double> rowCoords_;
  size_t nbrOfAxes_;
  std::string model_;
  std::vector<double> columnWeights_;
  std::map<std::string, std::string> paramValues_;
 
public:
  std::shared_ptr<const ProteicAlphabet> getProteicAlphabet() const override
  {
    return std::dynamic_pointer_cast<const ProteicAlphabet>(getAlphabet());
  }
 
  void setTransposeMatrixOfPpalAxes(const RowMatrix<double>& matrix) { tPpalAxes_ = matrix; }
  void setMatrixOfRowCoords(const RowMatrix<double>& matrix) { rowCoords_ = matrix; }
  void setNbrOfAxes(const size_t& nAxes) { nbrOfAxes_ = nAxes; }
  void setModelName(const std::string& modelName) { model_ = modelName; }
  void setVectorOfColumnWeights(const std::vector<double>& cw) { columnWeights_ = cw; }
  void setParamValues(std::map<std::string, std::string>& valuesSettings) {paramValues_ = valuesSettings;}
 
  void setFrequencies(const std::vector<double>& frequencies) override;
 
  void defineParameters();
  void fireParameterChanged(const ParameterList& parameters) override;
  void updateFrequencies();
 
  void initSet(const CoalaCore& coala);
 
  void computeReversePCA(const std::vector<double>& positions, std::vector<double>& tmpFreqs);
  void computeCoordsFirstSpacePCA(std::vector<double>& tmpFreqs, std::vector<double>& freqs);
  void computeReverseCOA(const std::vector<double>& positions, std::vector<double>& tmpFreqs);
  void computeCoordsFirstSpaceCOA(std::vector<double>& tmpFreqs, std::vector<double>& freqs);
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_FREQUENCYSET_MVAFREQUENCYSET_H