GeneticCode.h

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//
// File: GeneticCode.h
// Created by: Julien Dutheil
// Created on: Mon Oct 13 15:37:25 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 _GENETICCODE_H_
#define _GENETICCODE_H_

#include "../Transliterator.h"
#include "../Alphabet/CodonAlphabet.h"
#include "../Alphabet/ProteicAlphabet.h"
#include <Bpp/Exceptions.h>

namespace bpp
{

  class StopCodonException:
    public Exception
  {
  private:
    std::string codon_;
      
  public:
    // Class constructor
    StopCodonException(const std::string& text, const std::string& codon);
  
    // Class destructor
    virtual ~StopCodonException() throw () {}
    
  public:
    virtual const std::string& getCodon() const { return codon_; }
  };

  class GeneticCode:
    public AbstractTransliterator,
    public virtual Clonable
  {
  protected:
    CodonAlphabet codonAlphabet_;
    ProteicAlphabet proteicAlphabet_;
    std::map<int, int> tlnTable_;
  
  public:
    GeneticCode(const NucleicAlphabet* alphabet):
      AbstractTransliterator(),
      codonAlphabet_(alphabet),
      proteicAlphabet_(),
      tlnTable_()
    {}

    virtual ~GeneticCode() {}
  
    virtual GeneticCode* clone() const = 0;

  public:
    const CodonAlphabet* getSourceAlphabet() const { return &codonAlphabet_; }
    const ProteicAlphabet* getTargetAlphabet() const { return &proteicAlphabet_; }
    virtual int translate(int state) const throw (BadIntException, Exception);    
    virtual std::string translate(const std::string& state) const throw (BadCharException, Exception);
    virtual Sequence* translate(const Sequence& sequence) const throw (Exception)
    {
      return AbstractTransliterator::translate(sequence); 
    }
  public:
    virtual size_t getNumberOfStopCodons() const = 0;

    virtual std::vector<int> getStopCodonsAsInt() const = 0;

    virtual std::vector<std::string> getStopCodonsAsChar() const = 0;

    virtual bool isStop(int state) const throw (BadIntException) = 0;

    virtual bool isStop(const std::string& state) const throw (BadCharException) = 0;
    
    virtual bool isStart(int state) const throw (BadIntException) {
      //Test:
      codonAlphabet_.intToChar(state); //throw exception if invalid state!
      return (state == 14);
    }

    virtual bool isStart(const std::string& state) const throw (BadCharException) {
      return isStart(codonAlphabet_.charToInt(state));
    }
 
    virtual bool isAltStart(int state) const throw (BadIntException) = 0;

    virtual bool isAltStart(const std::string& state) const throw (BadCharException) = 0;
    
    bool areSynonymous(int i, int j) const throw (BadIntException)
    {
      return (translate(i) == translate(j));
    }

    bool areSynonymous(const std::string & i, const std::string & j) const throw (BadCharException)
    {
      return (translate(i) == translate(j));
    }

    std::vector<int> getSynonymous(int aminoacid) const throw (BadIntException);
    
    std::vector<std::string> getSynonymous(const std::string & aminoacid) const throw (BadCharException);

    bool isFourFoldDegenerated(int codon) const;

    Sequence* getCodingSequence(const Sequence& sequence, bool lookForInitCodon = false, bool includeInitCodon = false) const throw (Exception);
  };

} //end of namespace bpp.

#endif  //_GENETICCODE_H_