UserAlphabetIndex2.h

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

#ifndef BPP_SEQ_ALPHABETINDEX_USERALPHABETINDEX2_H
#define BPP_SEQ_ALPHABETINDEX_USERALPHABETINDEX2_H

#include <Bpp/Numeric/Matrix/MatrixTools.h>

#include "AlphabetIndex2.h"

// From the STL:
#include <vector>

namespace bpp
{
class UserAlphabetIndex2 :
  public virtual AlphabetIndex2
{
private:
  std::shared_ptr<const Alphabet> alph_;
  LinearMatrix<double> index_;
  bool sym_;

public:
  UserAlphabetIndex2(std::shared_ptr<const Alphabet> alph, const Matrix<double>& mat) :
    alph_(alph),
    index_(mat),
    sym_(false)
  {
    sym_ = MatrixTools::isSymmetric(index_);
  }

  UserAlphabetIndex2(const UserAlphabetIndex2& uAlph) :
    alph_(uAlph.alph_),
    index_(uAlph.index_),
    sym_(uAlph.sym_)
  {}

  UserAlphabetIndex2& operator=(const UserAlphabetIndex2& uAlph)
  {
    alph_  = uAlph.alph_;
    index_ = uAlph.index_;
    sym_ = uAlph.sym_;

    return *this;
  }

  virtual ~UserAlphabetIndex2() {}

  UserAlphabetIndex2* clone() const { return new UserAlphabetIndex2(*this); }

public:
  double getIndex(int state1, int state2) const
  {
    return index_(alph_->getStateIndex(state1) - 1, alph_->getStateIndex(state2) - 1);
  }

  double getIndex(const std::string& state1, const std::string& state2) const
  {
    return index_(alph_->getStateIndex(state1) - 1, alph_->getStateIndex(state2) - 1);
  }

  void setIndexMatrix(const Matrix<double>& mat)
  {
    index_ = mat;
    sym_ = MatrixTools::isSymmetric(index_);
  }

  LinearMatrix<double>* getIndexMatrix() const { return new LinearMatrix<double>(index_); }

  std::shared_ptr<const Alphabet> getAlphabet() const { return alph_; }
  
  const Alphabet& alphabet() const { return *alph_; }

  virtual bool isSymmetric() const
  {
    return sym_;
  }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_USERALPHABETINDEX2_H