DecompositionMethods.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_DECOMPOSITIONMETHODS_H
#define BPP_PHYL_MAPPING_DECOMPOSITIONMETHODS_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Numeric/Matrix/MatrixTools.h>
 
#include "../Model/SubstitutionModel.h"
#include "SubstitutionRegister.h"
 
namespace bpp
{
class DecompositionMethods
{
protected:
  std::shared_ptr<const SubstitutionModelInterface> model_;
  size_t nbStates_;
  size_t nbTypes_;
  mutable RowMatrix<double> jMat_, jIMat_;
 
  ColMatrix<double> rightEigenVectors_, rightIEigenVectors_;
  RowMatrix<double> leftEigenVectors_, leftIEigenVectors_;
 
  std::vector< RowMatrix<double>> bMatrices_, insideProducts_, insideIProducts_;
 
public:
  DecompositionMethods(
      std::shared_ptr<const SubstitutionModelInterface> model,
      std::shared_ptr<const SubstitutionRegisterInterface> reg);
 
  DecompositionMethods(std::shared_ptr<const SubstitutionRegisterInterface> reg);
 
  DecompositionMethods(std::shared_ptr<const SubstitutionModelInterface> model);
 
  DecompositionMethods(const StateMapInterface& stateMap);
 
  DecompositionMethods(const DecompositionMethods& dm) :
    model_(dm.model_),
    nbStates_(dm.nbStates_),
    nbTypes_(dm.nbTypes_),
    jMat_(dm.jMat_),
    jIMat_(dm.jIMat_),
    rightEigenVectors_(dm.rightEigenVectors_),
    rightIEigenVectors_(dm.rightIEigenVectors_),
    leftEigenVectors_(dm.leftEigenVectors_),
    leftIEigenVectors_(dm.leftIEigenVectors_),
    bMatrices_(dm.bMatrices_),
    insideProducts_(dm.insideProducts_),
    insideIProducts_(dm.insideIProducts_)
  {}
 
  DecompositionMethods& operator=(const DecompositionMethods& dm)
  {
    model_          = dm.model_;
    nbStates_       = dm.nbStates_;
    nbTypes_        = dm.nbTypes_;
    jMat_           = dm.jMat_;
    jIMat_          = dm.jIMat_;
 
    rightEigenVectors_ = dm.rightEigenVectors_;
    rightIEigenVectors_ = dm.rightIEigenVectors_;
    leftEigenVectors_ = dm.leftEigenVectors_;
    leftIEigenVectors_ = dm.leftIEigenVectors_;
    bMatrices_      = dm.bMatrices_;
    insideProducts_ = dm.insideProducts_;
    insideIProducts_ =  dm.insideIProducts_;
 
    return *this;
  }
 
  DecompositionMethods* clone() const { return new DecompositionMethods(*this); }
 
  virtual ~DecompositionMethods() {}
 
 
  void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model);
 
protected:
  void initStates_();
 
  void initBMatrices_();
 
  void computeProducts_();
 
  /*
   * @brief Perform the computation of the conditional expectations
   *
   */
 
  void computeExpectations(RowMatrix<double>& mapping, double length) const;
 
  void computeExpectations(std::vector< RowMatrix<double>>& mappings, double length) const;
 
  void jFunction_(const std::vector<double>& lambda, double t, RowMatrix<double>& result) const;
 
  void jFunction_(const std::vector<double>& lambda, const std::vector<double>& ilambda, double t, RowMatrix<double>& result, RowMatrix<double>& iresult) const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_DECOMPOSITIONMETHODS_H