GranthamAAChemicalDistance.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_SEQ_ALPHABETINDEX_GRANTHAMAACHEMICALDISTANCE_H
#define BPP_SEQ_ALPHABETINDEX_GRANTHAMAACHEMICALDISTANCE_H


// from the STL:
#include <string>

#include "AlphabetIndex2.h"
#include "../Alphabet/AlphabetExceptions.h"
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Matrix/Matrix.h>

namespace bpp
{
class GranthamAAChemicalDistance :
  public ProteicAlphabetIndex2
{
private:
  LinearMatrix<double> distanceMatrix_;
  LinearMatrix<double> signMatrix_;
  LinearMatrix<double> indexMatrix_;
  short int sign_;

public:
  GranthamAAChemicalDistance();

  GranthamAAChemicalDistance(const GranthamAAChemicalDistance& gd) :
    ProteicAlphabetIndex2(gd),
    distanceMatrix_(gd.distanceMatrix_),
    signMatrix_(gd.signMatrix_),
    indexMatrix_(gd.indexMatrix_),
    sign_(gd.sign_)
  {}

  GranthamAAChemicalDistance& operator=(const GranthamAAChemicalDistance& gd)
  {
    ProteicAlphabetIndex2::operator=(*this);

    distanceMatrix_ = gd.distanceMatrix_;
    signMatrix_ = gd.signMatrix_;
    indexMatrix_ = gd.indexMatrix_;
    sign_ = gd.sign_;
    return *this;
  }

  GranthamAAChemicalDistance* clone() const override { return new GranthamAAChemicalDistance(); }

  virtual ~GranthamAAChemicalDistance() {}

public:
  double getIndex(int state1, int state2) const override;
  double getIndex(const std::string& state1, const std::string& state2) const override;
  const Matrix<double>& getIndexMatrix() const override { return indexMatrix_; }
protected:
  void computeIndexMatrix_();

public:
  void setSymmetric(bool yn)
  {
    sign_ = (yn ? SIGN_NONE : SIGN_ARBITRARY);
    computeIndexMatrix_();
  }
  bool isSymmetric() const override { return sign_ == SIGN_NONE; }
  void setPC1Sign(bool yn)
  {
    sign_ = (yn ? SIGN_PC1 : SIGN_ARBITRARY);
    computeIndexMatrix_();
  }

  static short int SIGN_ARBITRARY;
  static short int SIGN_PC1;
  static short int SIGN_NONE;
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_GRANTHAMAACHEMICALDISTANCE_H