/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
#ifndef contigSegment_INCLUDED
#define contigSegment_INCLUDED

#include    "bool.h"

class contigSegment {
public:
   int nUnpaddedStart1_;
   int nUnpaddedEnd1_;

   int nUnpaddedStart2_;
   int nUnpaddedEnd2_;

   bool bBestContigIsContig1NotContig2_;


   // These are the padded positions relative to the new contig
   // which is also the left contig;
   // It includes any pads that have been
   // inserted for the purpose of aligning the 2 contigs.

   // these are made contiguous since there 
   // may be pads between the contigSegments

   int nNewPaddedStart_;
   int nNewPaddedEnd_;


   // needed for RWTValOrderedVector
   bool operator==( const contigSegment cs ) const {
      return( this == &cs );
   }

   // needed for RWTValOrderedVector
   void operator=( const contigSegment& cs ) {
      nUnpaddedStart1_ = cs.nUnpaddedStart1_;
      nUnpaddedEnd1_ = cs.nUnpaddedEnd1_;
      nUnpaddedStart2_ = cs.nUnpaddedStart2_;
      nUnpaddedEnd2_ = cs.nUnpaddedEnd2_;
      bBestContigIsContig1NotContig2_ = cs.bBestContigIsContig1NotContig2_;
      nNewPaddedStart_ = cs.nNewPaddedStart_;
      nNewPaddedEnd_ = cs.nNewPaddedEnd_;
   }

   // needed for RWTValOrderedVector
   contigSegment() {}
   
   // needed for RWTValOrderedVector
   contigSegment( const contigSegment& cs ) {
      nUnpaddedStart1_ = cs.nUnpaddedStart1_;
      nUnpaddedEnd1_ = cs.nUnpaddedEnd1_;
      nUnpaddedStart2_ = cs.nUnpaddedStart2_;
      nUnpaddedEnd2_ = cs.nUnpaddedEnd2_;
      bBestContigIsContig1NotContig2_ = cs.bBestContigIsContig1NotContig2_;
      nNewPaddedStart_ = cs.nNewPaddedStart_;
      nNewPaddedEnd_ = cs.nNewPaddedEnd_;
   }
      

};


#endif