Codon.h

#ifndef theplu_yat_omic_codon
#define theplu_yat_omic_codon

// $Id: Codon.h 3487 2016-03-24 04:24:05Z peter $

/*
  Copyright (C) 2010, 2011, 2012, 2013, 2016 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "DNA.h"

#include <functional>
#include <map>
#include <string>
#include <vector>

namespace theplu {
namespace yat {
namespace omic {

  class Codon
  {
  public:
    Codon(void);

    Codon(const std::string& str);

    Codon(const DNA& first, const DNA& second, const DNA& third);

    char amino_acid(void) const;

    std::string amino_acid_long(void) const;

    const DNA& operator()(size_t i) const;

    bool start(void) const;

    bool stop(void) const;
  private:
    struct Compare_
    {
      bool operator()(const std::vector<DNA>& lhs,
                      const std::vector<DNA>& rhs) const;
    };
    typedef std::map<std::vector<DNA>, char, Compare_> Map_;
    static Map_ map_;

    Map_::const_iterator iter_;

    void add_to_map(char aa, const std::string& codons);

    void init(const std::vector<DNA>& vec);
    void create_map(void);

    // using compiler generated copy
    // Codon(const Codon&)
    // Codon& operator=(const Codon&)
  };

  struct AminoAcidEqual : public std::binary_function<Codon, Codon, bool>
  {
    bool operator()(const Codon& lhs, const Codon& rhs) const;
  };

}}}
#endif