/*****************************************************************************
#   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    "contigEndPair.h"
#include    "contig.h"
#include    "contigEnd.h"
#include    "rwcstring.h"



contigEndPair :: contigEndPair( Contig* pContig0,
                                Contig* pContig1,
                                const int nWhichEnd0,
                                const int nWhichEnd1 ) :
      pChoiceOfTemplatesForMinilibraries_( NULL ),
      pArrayOfTemplates_( NULL ),
      bInconsistent_( false ),
      bAlreadySuggestedMinilibrariesForThisGap_( false ),
      bUserDefined_( false ),
      bGapSizeSet_( false ),
      nGapSize_( 0 ),
      nHighQualityGapSize_( 0 ),
      nNumberOfForwardReversePairs_( 0 ) {

   if ( pContig0->soGetName() < pContig1->soGetName() ) {
      pContig_[0] = pContig0;
      pContig_[1] = pContig1;
      nWhichEnd_[0] = nWhichEnd0;
      nWhichEnd_[1] = nWhichEnd1;
   }
   else {
      pContig_[0] = pContig1;
      pContig_[1] = pContig0;
      nWhichEnd_[0] = nWhichEnd1;
      nWhichEnd_[1] = nWhichEnd0;
   }

   pTag_[0] =  NULL;
   pTag_[1] =  NULL;

}


void contigEndPair :: recordTags( tag* pTag0, tag* pTag1 ) {

   if ( pTag0->pContig_->soGetName() < pTag1->pContig_->soGetName() ) {
      pTag_[0] = pTag0;
      pTag_[1] = pTag1;
   }
   else {
      pTag_[0] = pTag1;
      pTag_[1] = pTag0;
   }
}





RWCString contigEndPair :: soGetDescription() {

   RWCString soDescription( (size_t) 300 );

   for( int nEnd = 0; nEnd <= 1; ++nEnd ) {
      soDescription += pContig_[nEnd]->soGetName();
      soDescription += " ";
      soDescription += szWhichGap( nWhichEnd_[ nEnd ] );

      if ( nEnd == 0 ) {
         soDescription += " to ";
      }
   }


   // now put it in the format A-B or Ac-B or A-Bc

   soDescription += "  (";
   if ( nWhichEnd_[0] != nWhichEnd_[1] ) {
      // case in which neither contig needs to be complemented

      if ( nWhichEnd_[0] == nLeftGap ) {
         // so want 1-0 
         
         soDescription += pContig_[1]->soGetAbbreviatedName();
         soDescription += "-";
         soDescription += pContig_[0]->soGetAbbreviatedName();
      }
      else {
         soDescription += pContig_[0]->soGetAbbreviatedName();
         soDescription += "-";
         soDescription += pContig_[1]->soGetAbbreviatedName();
      }
   }
   else {
      // case in which one of the contigs must be complemented

      int nIndexOfLargerContig = ( pContig_[0]->nGetPaddedConsLength()
                                   >
                                   pContig_[1]->nGetPaddedConsLength() ?
                                   0 : 1 );

      int nIndexOfSmallerContig = ( nIndexOfLargerContig == 0 ?
                                    1 : 0 );

      if ( nWhichEnd_[0] == nLeftGap ) {
         
         // there are two possibilities:  1c-0 or 0c-1
         // let's choose between them based on which contig is larger

         soDescription += pContig_[nIndexOfSmallerContig]->soGetAbbreviatedName();
         soDescription += "c-";
         soDescription += pContig_[nIndexOfLargerContig]->soGetAbbreviatedName();
      }
      else {
         
         // there are two possibilities 0-1c or 1-0c
         // let's choose between them based on which contig is larger

         soDescription += pContig_[nIndexOfLargerContig]->soGetAbbreviatedName();
         soDescription += "-";
         soDescription += pContig_[nIndexOfSmallerContig]->soGetAbbreviatedName();
         soDescription += "c";
      }
   }
   soDescription += ")";

   return( soDescription );
}


void contigEndPair :: calculateHighQualityGapSize() {

   // this assumes that nGapSize_ is already set

   nHighQualityGapSize_ = nGapSize_;

   for( int nContigEnd = 0; nContigEnd <= 1; ++nContigEnd ) {

      Contig* pContig = pContig_[ nContigEnd ];
      int nWhichEnd = nWhichEnd_[ nContigEnd ];
      
      int nLowQualityBases = 
         pContig->nGetUnpaddedClippedLowQualityBases( nWhichEnd );

      nHighQualityGapSize_ += nLowQualityBases;
   }

   assert( nHighQualityGapSize_ >= nGapSize_ );

}


void contigEndPair :: makeAllTemplatesConsistent() {

   if ( pArrayOfTemplates_ ) {
      for( int nSub = 0; nSub < pArrayOfTemplates_->length(); ++nSub ) {
         subcloneTTemplate* pSub = (*pArrayOfTemplates_)[ nSub ];

         pSub->bInconsistentGapSpanning_ = false;

         pSub->determineIfOKToUseTemplate();
      }
   }
}