AAChargeIndex.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_AACHARGEINDEX_H
#define BPP_SEQ_ALPHABETINDEX_AACHARGEINDEX_H
 
 
#include "AlphabetIndex1.h"
 
namespace bpp
{
class AAChargeIndex :
  public ProteicAlphabetIndex1
{
private:
  std::vector<double> charge_;
 
public:
  AAChargeIndex() :
    ProteicAlphabetIndex1(),
    charge_()
  {
    charge_.resize(20);
    charge_[ 0] =  0.; // A
    charge_[ 1] =  1.; // R
    charge_[ 2] =  0.; // N
    charge_[ 3] = -1.; // D
    charge_[ 4] =  0.; // C
    charge_[ 5] =  0.; // Q
    charge_[ 6] = -1.; // E
    charge_[ 7] =  0.; // G
    charge_[ 8] =  1.; // H
    charge_[ 9] =  0.; // I
    charge_[10] =  0.; // L
    charge_[11] =  1.; // K
    charge_[12] =  0.; // M
    charge_[13] =  0.; // F
    charge_[14] =  0.; // P
    charge_[15] =  0.; // S
    charge_[16] =  0.; // T
    charge_[17] =  0.; // W
    charge_[18] =  0.; // Y
    charge_[19] =  0.; // V
  }
 
  virtual ~AAChargeIndex() {}
 
  AAChargeIndex* clone() const override { return new AAChargeIndex(); }
 
public:
  double getIndex(int state) const override
  {
    return charge_[getAlphabet()->getStateIndex(state) - 1];
  }
 
  double getIndex(const std::string& state) const override
  {
    return charge_[getAlphabet()->getStateIndex(state) - 1];
  }
 
  const std::vector<double>& indexVector() const override { return charge_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_AACHARGEINDEX_H