DNA.h

#ifndef theplu_yat_omic_dna
#define theplu_yat_omic_dna

/*
  $Id: DNA.h 2577 2011-10-03 13:53:55Z peter $

  Copyright (C) 2010, 2011 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 <boost/operators.hpp>

#include <iosfwd>
#include <map>
#include <string>
#include <vector>

namespace theplu {
namespace yat {
namespace omic {

  class DNA : boost::operators<DNA>
  {
  public:
    DNA(void);

    DNA(const DNA&);

    explicit DNA(char c);

    DNA complement(void) const;

    char get(void) const;

    DNA& operator&=(const DNA& rhs);

    DNA& operator|=(const DNA& rhs);

    DNA& operator^=(const DNA& rhs);

    DNA& operator=(char c);

  private:
    unsigned short code_;
    static std::map<char, unsigned short> char2code_;
    static std::vector<char> code2char_;

    void init(void) const;

    friend bool operator==(const DNA&, const DNA&);
};  

  std::string expand(const DNA&);

  bool operator==(const DNA& lhs, const DNA& rhs);

  std::ostream& operator<<(std::ostream& os, const DNA& dna);
}}}
#endif