source: trunk/yat/omic/GenomicPosition.cc @ 2366

// $Id: GenomicPosition.cc 2366 2010-12-06 02:17:02Z peter $

/*
  Copyright (C) 2010 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 "GenomicPosition.h"

#include "yat/utility/utility.h"

#include <string>

namespace theplu {
namespace yat {
namespace omic {

  GenomicPosition::GenomicPosition(void) 
  {}


  GenomicPosition::GenomicPosition(unsigned short int chr, unsigned long int pos)
    : chr_(chr), pos_(pos)
  {}


  GenomicPosition::GenomicPosition(const std::string& chr, const std::string& pos)
    : chr_(chr2int(chr)), 
      pos_(yat::utility::convert<unsigned long int>(pos))
  {}


  unsigned short& GenomicPosition::chromosome(void)
  { return chr_; }


  const unsigned short& GenomicPosition::chromosome(void) const
  { return chr_; }


  unsigned long int& GenomicPosition::position(void)
  { return pos_; }


  const unsigned long int& GenomicPosition::position(void) const
  { return pos_; }


  bool operator<(const GenomicPosition& lhs, const GenomicPosition& rhs)
  {
    if (lhs.chromosome()==rhs.chromosome())
      return lhs.position() < rhs.position();
    return lhs.chromosome() < rhs.chromosome();
  }


  bool operator==(const GenomicPosition& lhs, const GenomicPosition& rhs)
  {
    return lhs.chromosome()==rhs.chromosome() && lhs.position()==rhs.position();
  }


  unsigned short chr2int(const std::string& str)
  {
    if (str.size()>3 && str.substr(0,3)=="chr")
      return chr2int(str.substr(3));
    if (str=="X")
      return 23;
    if (str=="Y")
      return 24;
    if (str=="M" || str=="MT")
      return 25;
    return utility::convert<unsigned short>(str);
  }
}}}