GenomicPosition.h

#ifndef theplu_yat_omic_gemomic_position
#define theplu_yat_omic_gemomic_position

// $Id: GenomicPosition.h 3114 2013-11-10 23:51:47Z peter $

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

  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 this program. If not, see <http://www.gnu.org/licenses/>.
*/

#include <boost/operators.hpp>

#include <string>

namespace theplu {
namespace yat {
namespace omic {

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

    GenomicPosition(unsigned short chr , unsigned long pos);

    GenomicPosition(const std::string& chr, const std::string& pos);

    unsigned short& chromosome(void);

    const unsigned short& chromosome(void) const;

    unsigned long int& position(void);

    const unsigned long int& position(void) const;

  private:
    unsigned short chr_;
    unsigned long pos_;
  };

  bool operator<(const GenomicPosition& lhs, const GenomicPosition& rhs);

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

  unsigned short chr2int(const std::string& str);

}}}
#endif