GranthamAAChemicalDistance.h

Go to the documentation of this file.

// 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