KD_AAHydropathyIndex.h

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

#ifndef BPP_SEQ_ALPHABETINDEX_KD_AAHYDROPATHYINDEX_H
#define BPP_SEQ_ALPHABETINDEX_KD_AAHYDROPATHYINDEX_H


#include "AlphabetIndex1.h"

namespace bpp
{
class KD_AAHydropathyIndex :
  public virtual ProteicAlphabetIndex1
{
private:
  std::vector<double> hydropathy_;

public:
  KD_AAHydropathyIndex() :
    ProteicAlphabetIndex1(),
    hydropathy_()
  {
    hydropathy_.resize(20);
    hydropathy_[ 0] = 1.8; // A
    hydropathy_[ 1] = -4.5; // R
    hydropathy_[ 2] = -3.5; // N
    hydropathy_[ 3] = -3.5; // D
    hydropathy_[ 4] = 2.5; // C
    hydropathy_[ 5] = -3.5; // Q
    hydropathy_[ 6] = -3.5; // E
    hydropathy_[ 7] = -0.4; // G
    hydropathy_[ 8] = -3.2; // H
    hydropathy_[ 9] = 4.5; // I
    hydropathy_[10] = 3.8; // L
    hydropathy_[11] = -3.9; // K
    hydropathy_[12] = 1.9; // M
    hydropathy_[13] = 2.8; // F
    hydropathy_[14] = -1.6; // P
    hydropathy_[15] = -0.8; // S
    hydropathy_[16] = -0.7; // T
    hydropathy_[17] = -0.9; // W
    hydropathy_[18] = -1.3; // Y
    hydropathy_[19] = 4.2; // V
  }

  virtual ~KD_AAHydropathyIndex() {}

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

public:
  double getIndex(int state) const override
  {
    return hydropathy_[getAlphabet()->getStateIndex(state) - 1];
  }

  double getIndex(const std::string& state) const override
  {
    return hydropathy_[getAlphabet()->getStateIndex(state) - 1];
  }

  const std::vector<double>& indexVector() const override { return hydropathy_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_KD_AAHYDROPATHYINDEX_H