GranthamAAVolumeIndex.h

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

#ifndef BPP_SEQ_ALPHABETINDEX_GRANTHAMAAVOLUMEINDEX_H
#define BPP_SEQ_ALPHABETINDEX_GRANTHAMAAVOLUMEINDEX_H


#include "AlphabetIndex1.h"

// From the STL:
#include <vector>

namespace bpp
{
class GranthamAAVolumeIndex :
  public virtual ProteicAlphabetIndex1
{
private:
  std::vector<double> volume_;

public:
  GranthamAAVolumeIndex() :
    ProteicAlphabetIndex1(),
    volume_()
  {
    volume_.resize(20);
    volume_[ 0] =  31.; // A
    volume_[ 1] = 124.; // R
    volume_[ 2] =  56.; // N
    volume_[ 3] =  54.; // D
    volume_[ 4] =  55.; // C
    volume_[ 5] =  85.; // Q
    volume_[ 6] =  83.; // E
    volume_[ 7] =   3.; // G
    volume_[ 8] =  96.; // H
    volume_[ 9] = 111.; // I
    volume_[10] = 111.; // L
    volume_[11] = 119.; // K
    volume_[12] = 105.; // M
    volume_[13] = 132.; // F
    volume_[14] =  32.5; // P
    volume_[15] =  32.; // S
    volume_[16] =  61.; // T
    volume_[17] = 170.; // W
    volume_[18] = 136.; // Y
    volume_[19] =  84.; // V
  }

  virtual ~GranthamAAVolumeIndex() {}

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

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

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

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