/*****************************************************************************
#   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 contigEndPair_included
#define contigEndPair_included


#include    "subcloneTTemplate.h"

class templateForMinilibrary;
class Contig;


class contigEndPair {
public:
   Contig* pContig_[2];
   int nWhichEnd_[2];
   tag* pTag_[2]; // not always used
   // if this end is the clone end,
   // then this flag will be set and pContig_[1] will be null

   bool bUserDefined_; // not based on forward-reverse pairs

   int nNumberOfForwardReversePairs_;

   bool bInconsistent_;

   bool bGapSizeSet_;
   int nGapSize_;
   int nHighQualityGapSize_; // larger than above since this gap includes
        // the low quality ends of the 2 contigs going into the gap

   bool bAlreadySuggestedMinilibrariesForThisGap_;
   RWTPtrOrderedVector<templateForMinilibrary>* pChoiceOfTemplatesForMinilibraries_;
   // pChoiceOfTemplatesForMinilibraries_ is only used if there are
   // minilibraries suggested.

   RWTValOrderedVector<subcloneTTemplate*>* pArrayOfTemplates_;
   // this is used to list all templates that span the gap.

public:

   // I may, at some point, change this so that it checks 
   // that the contigs are the same and the ends are the same.
   // That would be more useful for two objects that represent
   // the same contig end pair.
   bool operator==( const contigEndPair& pair ) const {
      if ( pContig_[0] == pair.pContig_[0] &&
           pContig_[1] == pair.pContig_[1] && 
           nWhichEnd_[0] == pair.nWhichEnd_[0] && 
           nWhichEnd_[1] == pair.nWhichEnd_[1] ) 
         return( true );
      else
         return( false );
   }


   contigEndPair( Contig* pContig0,
                  Contig* pContig1,
                  const int nWhichEnd0,
                  const int nWhichEnd1 );

   // for RWTValOrderedVector
   contigEndPair() {
      pContig_[0] = NULL;
      pContig_[1] = NULL;
      nWhichEnd_[0] = -666;
      nWhichEnd_[1] = -666;
      bUserDefined_ = false;
      bGapSizeSet_ = false;
   }

   RWCString soGetDescription();

   void recordTags( tag* pTag1, tag* pTag2 );

   void calculateHighQualityGapSize();

   void makeAllTemplatesConsistent();

};




#endif