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

#ifndef theplu_yat_omic_gemomic_position
#define theplu_yat_omic_gemomic_position

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

  Copyright (C) 2010, 2012 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 used to hold genomic location, i.e., chromosome and
     position.

     The class inherits from boost::operators, which means besides the
     operators directly implemented (operator== and operator<) also
     operator<=, operator>, operator>=, and operator!= are supported.

     \since New in yat 0.7
   */
  class GenomicPosition : boost::operators<GenomicPosition>
  {
  public:
    /**
       Creates a GenomicPosition with undefined values.
     */
    GenomicPosition(void);

    /**
       \brief Constructor
       \param chr chromosome
       \param pos non-negative number describing location on chromosome
     */
    GenomicPosition(unsigned short chr , unsigned long pos);

    /**
       \brief Constructor
       \param chr chromosome
       \param pos non-negative number describing location on chromosome

       chr2int is used to translate \a chr into an \c unsigned \c
       short, and utility::convert is used to translate \a pos into an
       \c unsigned \c long.

       \see chr2int
     */
    GenomicPosition(const std::string& chr, const std::string& pos);

    /**
       \return reference to chr
     */
    unsigned short& chromosome(void);

    /**
       \return const reference to chr
     */
    const unsigned short& chromosome(void) const;

    /**
       \return reference to position
     */
    unsigned long int& position(void);

    /**
       \return const reference to position
     */
    const unsigned long int& position(void) const;

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

  /**
     \relates GenomicPosition

     \return \c true if chromosome of \a lhs is less than chromosome
     of \a rhs or if chromosome of \a lhs equals chromosome of \a rhs
     and position of \a lhs is less than position of \a rhs.

     \since New in yat 0.7
   */
  bool operator<(const GenomicPosition& lhs, const GenomicPosition& rhs);

  /**
     \relates GenomicPosition

     \return \c true if chromosomes and positions are the same.

     \since New in yat 0.7
   */
  bool operator==(const GenomicPosition& lhs, const GenomicPosition& rhs);

  /**
     \brief transform a string to unsigned short chromosome number

     If \a str starts with 'chr' that prefix is stripped away before
     translating the string to chromosome number. Function translates
     "X" to 23, "Y" to 24, and "M" or "MT" to 25. For other inputs
     utility::convert is used to transform the input to an unsigned
     short.

     \return chromosome number

     \since New in yat 0.7
   */
  unsigned short chr2int(const std::string& str);

}}}
#endif