/* SAMRecordComparator
 *
 * created: 2009
 *
 * This file is part of Artemis
 *
 * Copyright(C) 2009  Genome Research Limited
 *
 * This program 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 2
 * of the License, or(at your option) any later version.
 *
 * This program 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, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

package uk.ac.sanger.artemis.components.alignment;

import java.util.Comparator;

import net.sf.samtools.SAMRecord;

import uk.ac.sanger.artemis.components.alignment.BamView.PairedRead;


  class PairedReadComparator implements Comparator<Object>
  {
    public int compare(Object o1, Object o2) 
    {
      SAMRecord sam1 = ((PairedRead) o1).sam1.sam;
      SAMRecord sam2 = ((PairedRead) o2).sam1.sam;
      
      int start1 = sam1.getAlignmentStart();
      if(sam1.getAlignmentEnd() < start1)
        start1 = sam1.getAlignmentEnd();
      
      int start2 = sam2.getAlignmentStart();
      if(sam2.getAlignmentEnd() < start2)
        start2 = sam1.getAlignmentEnd();
        
      return start1-start2;
    }
  }