source: trunk/yat/omic/Codon.h @ 2919

#ifndef theplu_yat_omic_codon
#define theplu_yat_omic_codon

/*
  $Id: Codon.h 2919 2012-12-19 06:54:23Z peter $

  Copyright (C) 2010, 2011, 2012 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 holding a triplet of DNAs that are translated to an amino acid.

     <table>
     <tr><td>Ala</td><td>A</td><td>GCT,GCC,GCA,GCG</td></tr>
     <tr><td>Leu</td><td>L</td><td>TTA,TTG,CTT,CTC,CTA,CTG</td></tr>
     <tr><td>Arg</td><td>R</td><td>CGT,CGC,CGA,CGG,AGA,AGG</td></tr>
     <tr><td>Lys</td><td>K</td><td>AAA,AAG</td></tr>
     <tr><td>Asn</td><td>N</td><td>AAT,AAC</td></tr>
     <tr><td>Met</td><td>M</td><td>ATG</td></tr>
     <tr><td>Asp</td><td>D</td><td>GAT,GAC</td></tr>
     <tr><td>Phe</td><td>F</td><td>TTT,TTC</td></tr>
     <tr><td>Cys</td><td>C</td><td>TGT,TGC</td></tr>
     <tr><td>Pro</td><td>P</td><td>CCT,CCC,CCA,CCG</td></tr>
     <tr><td>Gln</td><td>Q</td><td>CAA,CAG</td></tr>
     <tr><td>Ser</td><td>S</td><td>TCT,TCC,TCA,TCG,AGT,AGC</td></tr>
     <tr><td>Glu</td><td>E</td><td>GAA,GAG</td></tr>
     <tr><td>Thr</td><td>T</td><td>ACT,ACC,ACA,ACG</td></tr>
     <tr><td>Gly</td><td>G</td><td>GGT,GGC,GGA,GGG</td></tr>
     <tr><td>Trp</td><td>W</td><td>TGG</td></tr>
     <tr><td>His</td><td>H</td><td>CAT,CAC</td></tr>
     <tr><td>Tyr</td><td>Y</td><td>TAT,TAC</td></tr>
     <tr><td>Ile</td><td>I</td><td>ATT,ATC,ATA</td></tr>
     <tr><td>Val</td><td>V</td><td>GTT,GTC,GTA,GTG</td></tr>
     <tr><td>START</td><td></td><td>ATG</td></tr>
     <tr><td>STOP</td>*<td></td><td>TAA,TGA,TAG</td></tr>
     </table>

     \since New in yat 0.7
   */
  class Codon
  {
  public:
    /**
       \brief Defaulf constructor.

       Value is undefined
     */
    Codon(void);

    /**
       \a str must be three characters long and each character must be
       convertible to a DNA.

       \see DNA
     */
    Codon(const std::string& str);

    /**
       Create Codon from three DNA
     */
    Codon(const DNA& first, const DNA& second, const DNA& third);

    /**
       \return one character describing which amino acid the Codon
       translates to.
     */
    char amino_acid(void) const;

    /**
       \return \a i th DNA
     */
    const DNA& operator()(size_t i) const;

    /**
       \return \c true if Codon is a start Codon: "ATG"
     */
    bool start(void) const;

    /**
       \return \c true if Codon is a stop codon (see class docs).
     */
    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&)
  };

  /**
     \brief Functor comparing if two Codons translate to the same amino acid

     \relates Codon

     \since New in yat 0.7
   */
  struct AminoAcidEqual : public std::binary_function<Codon, Codon, bool>
  {
    /// \return \c true \a lhs and \a rhs translates to same amino acid
    bool operator()(const Codon& lhs, const Codon& rhs) const;
  };

}}}
#endif