/*****************************************************************************
#   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.
#
#*****************************************************************************/
#include    "bForwardReversePairIsConsistentWithContigOrder.h"
#include    "locatedFragment.h"
#include    "contig.h"
#include    "assert.h"
#include    "fwdRevPair2.h"


// note that this will only work if
// Contig::bThisContigIsComplementedInTheScaffold_ and
// Contig::nClonePosLeft_ are set.  Former is set by
// calling Assembly :: figureOutContigOrderAndOrientation() and
// the latter by Assembly::getScaffoldBases



bool bForwardReversePairIsConsistentWithContigOrder( 
             LocatedFragment* pForwardLocFrag,
             LocatedFragment* pReverseLocFrag,
             char& cProblem ) {


   // this is not what we are checking
   if ( pForwardLocFrag->pGetContig() == pReverseLocFrag->pGetContig() )
      return( true );
                                      

   // this is also not what we are checking
   if ( pForwardLocFrag->pGetContig()->nScaffold_ !=
        pReverseLocFrag->pGetContig()->nScaffold_ )
      return( true );

   LocatedFragment* pLeftLocFrag;
   LocatedFragment* pRightLocFrag;

   if ( pForwardLocFrag->pGetContig()->nClonePosLeft_ <
        pReverseLocFrag->pGetContig()->nClonePosLeft_ ) {
      
      pLeftLocFrag = pForwardLocFrag;
      pRightLocFrag = pReverseLocFrag;
   }
   else {
      pLeftLocFrag = pReverseLocFrag;
      pRightLocFrag = pForwardLocFrag;
   }

   // if reached here, the reads are in different contigs within the
   // same scaffold.  Make sure they are pointing towards each other
   // within the scaffold.

   bool bLeftLocFragPointsRight;
   bool bRightLocFragPointsRight;

   if ( pLeftLocFrag->bComp() )
      bLeftLocFragPointsRight = false;
   else
      bLeftLocFragPointsRight = true;

   if ( pRightLocFrag->bComp() )
      bRightLocFragPointsRight = false;
   else
      bRightLocFragPointsRight = true;

   if ( pLeftLocFrag->pGetContig()->bThisContigIsComplementedInTheScaffold_ )
      bLeftLocFragPointsRight = !bLeftLocFragPointsRight;

   if ( pRightLocFrag->pGetContig()->bThisContigIsComplementedInTheScaffold_ )
      bRightLocFragPointsRight = !bRightLocFragPointsRight;

   if ( bLeftLocFragPointsRight && bRightLocFragPointsRight ) {
      cProblem = fwdRevPair2::cBOTH_POINT_RIGHT;
      return( false );
   }
   else if ( !bLeftLocFragPointsRight && !bRightLocFragPointsRight ) {
      cProblem = fwdRevPair2::cBOTH_POINT_LEFT;
      return( false );
   }
   else if ( !bLeftLocFragPointsRight && bRightLocFragPointsRight ) {
      cProblem = fwdRevPair2::cPOINT_AWAY_FROM_EACH_OTHER;
      return( false );
   }
   else if ( bLeftLocFragPointsRight && !bRightLocFragPointsRight ) {
      return( true );
   }
   else
      assert( false );

}