CodonFromProteicAlphabetIndex2.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_CODONFROMPROTEICALPHABETINDEX2_H
#define BPP_SEQ_ALPHABETINDEX_CODONFROMPROTEICALPHABETINDEX2_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
 
#include "../Alphabet/CodonAlphabet.h"
#include "../GeneticCode/GeneticCode.h"
#include "AlphabetIndex2.h"
 
namespace bpp
{
/*
 * @brief AlphabetIndex2 for codon based on ProteicAlphabetIndex2.
 *
 */
 
class CodonFromProteicAlphabetIndex2 :
  public AlphabetIndex2
{
private:
  std::shared_ptr<const CodonAlphabet> alpha_;
  std::shared_ptr<const GeneticCode> gencode_;
 
  LinearMatrix<double> vIndex_;
 
  bool isSymmetric_;
 
public:
  CodonFromProteicAlphabetIndex2(std::shared_ptr<const GeneticCode> gencode, std::shared_ptr<const AlphabetIndex2> protalphindex) :
    AlphabetIndex2(),
    alpha_(AlphabetTools::DNA_CODON_ALPHABET),
    gencode_(gencode),
    vIndex_(64, 64),
    isSymmetric_(protalphindex->isSymmetric())
  {
    if (!AlphabetTools::isProteicAlphabet(protalphindex->alphabet()))
      throw Exception("CodonFromProteicAlphabetIndex2: Not a Proteic Alphabet for CodonAlphabetIndex2.");
    fillIndex_(protalphindex);
  }
 
  CodonFromProteicAlphabetIndex2(const CodonFromProteicAlphabetIndex2& cfp) :
    alpha_(cfp.alpha_),
    gencode_(cfp.gencode_),
    vIndex_(cfp.vIndex_),
    isSymmetric_(cfp.isSymmetric_)
  {}
 
  CodonFromProteicAlphabetIndex2& operator=(const CodonFromProteicAlphabetIndex2& cfp)
  {
    alpha_ = cfp.alpha_;
    gencode_ = cfp.gencode_;
    vIndex_ = cfp.vIndex_;
    isSymmetric_ = cfp.isSymmetric_;
 
    return *this;
  }
 
  virtual ~CodonFromProteicAlphabetIndex2() {}
 
  CodonFromProteicAlphabetIndex2* clone() const override { return new CodonFromProteicAlphabetIndex2(*this); }
 
public:
  double getIndex(int state1, int state2) const override
  {
    return vIndex_(getAlphabet()->getStateIndex(state1) - 1, getAlphabet()->getStateIndex(state2) - 1);
  }
 
  double getIndex(const std::string& state1, const std::string& state2) const override
  {
    return vIndex_(getAlphabet()->getStateIndex(state1) - 1, getAlphabet()->getStateIndex(state2) - 1);
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override
  {
    return alpha_;
  }
 
  const Alphabet& alphabet() const override
  {
    return *alpha_;
  }
 
  const Matrix<double>& getIndexMatrix() const override
  {
    return vIndex_;
  }
 
  bool isSymmetric() const override
  {
    return isSymmetric_;
  }
 
private:
  void fillIndex_(std::shared_ptr<const AlphabetIndex2>& protAlphIndex_)
  {
    for (int i = 0; i < 64; i++)
    {
      for (int j = 0; j < 64; j++)
      {
        vIndex_(getAlphabet()->getStateIndex(i) - 1, getAlphabet()->getStateIndex(j) - 1) =
            gencode_->isStop(i) ? 0 :
            gencode_->isStop(j) ? 0 :
            protAlphIndex_->getIndex(gencode_->translate(i), gencode_->translate(j));
      }
    }
  }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_CODONFROMPROTEICALPHABETINDEX2_H