CodonAlphabet.h

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//
// File: CodonAlphabet.h
// Created by: Julien Dutheil
// Created on: Sun Oct 12 17:41:56 2003
//

/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

This software is a computer program whose purpose is to provide classes
for sequences analysis.

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".

As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided
only with a limited warranty and the software's author, the holder of
the economic rights, and the successive licensors have only limited
liability.

In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards
their requirements in conditions enabling the security of their
systems and/or data to be ensured and, more generally, to use and
operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _CODONALPHABET_H_
#define _CODONALPHABET_H_

#include "WordAlphabet.h"
#include "NucleicAlphabet.h"

// From the STL:
#include <string>


namespace bpp
{

class CodonAlphabet:
  public WordAlphabet
{
public: // Constructor and destructor.
    
  CodonAlphabet(const NucleicAlphabet* alpha) :
    WordAlphabet(alpha, 3) {}

  CodonAlphabet(const CodonAlphabet& bia) : WordAlphabet(bia) {}

  CodonAlphabet& operator=(const CodonAlphabet& bia)
  {
    WordAlphabet::operator=(bia);
    return *this;
  }
  
  CodonAlphabet* clone() const
  {
    return new CodonAlphabet(*this);
  }

  virtual ~CodonAlphabet() {}
  
  std::string getAlphabetType() const
  {
    return "Codon alphabet("+ vAbsAlph_[0]->getAlphabetType() + ")";
  }

  
public:
  
  virtual int getCodon(int pos1, int pos2, int pos3) const throw (BadIntException);
  
  virtual std::string getCodon(const std::string& pos1, const std::string& pos2, const std::string& pos3) const throw (BadCharException);
  
  virtual int getFirstPosition(int codon) const throw (BadIntException);
  
  virtual int getSecondPosition(int codon) const throw (BadIntException);
  
  virtual int getThirdPosition(int codon) const throw (BadIntException);
  
  virtual std::string getFirstPosition (const std::string& codon) const throw (BadCharException);
  
  virtual std::string getSecondPosition(const std::string& codon) const throw (BadCharException);
  
  virtual std::string getThirdPosition(const std::string& codon) const throw (BadCharException);
  
  virtual const NucleicAlphabet* const getNucleicAlphabet() const
  {
    return dynamic_cast<const NucleicAlphabet*>(vAbsAlph_[0]);
  }
  
};

} //end of namespace bpp.

#endif  //_CODONALPHABET_H_