AAIndex2Entry.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_AAINDEX2ENTRY_H
#define BPP_SEQ_ALPHABETINDEX_AAINDEX2ENTRY_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
 
#include "AlphabetIndex2.h"
 
namespace bpp
{
class AAIndex2Entry :
  public virtual ProteicAlphabetIndex2
{
private:
  LinearMatrix<double> property_;
  bool sym_;
 
public:
  AAIndex2Entry(std::istream& input, bool sym = true);
 
  AAIndex2Entry(const AAIndex2Entry& index) :
    ProteicAlphabetIndex2(*this),
    property_(index.property_),
    sym_(index.sym_)
  {}
 
  AAIndex2Entry& operator=(const AAIndex2Entry& index)
  {
    ProteicAlphabetIndex2::operator=(*this);
 
    property_ = index.property_;
    sym_ = index.sym_;
    return *this;
  }
 
  virtual ~AAIndex2Entry() {}
 
public:
  AAIndex2Entry* clone() const override { return new AAIndex2Entry(*this); }
 
  double getIndex(int state1, int state2) const override
  {
    return property_(getAlphabet()->getStateIndex(state1) - 1, getAlphabet()->getStateIndex(state2) - 1);
  }
 
  double getIndex(const std::string& state1, const std::string& state2) const override
  {
    return property_(getAlphabet()->getStateIndex(state1) - 1, getAlphabet()->getStateIndex(state2) - 1);
  }
 
  const Matrix<double>& getIndexMatrix() const override { return property_; }
 
  bool isSymmetric() const override { return sym_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_AAINDEX2ENTRY_H