/*****************************************************************************
#   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    "copyPrimerMatchesFromShorterToLongerPrimers.h"
#include    "primerType.h"
#include    "sortPrimersByEndPosition.h"
#include    "sortPrimersByStartPosition.h"
#include    "consedParameters.h"
#include    "assert.h"


// copySinglePrimerField takes
// copySinglePrimerField( nScoreOfStickiestFalseMatch_ )
// and makes

//          pPrimer->nScoreOfStickiestFalseMatch_ = shortPrimer.nScoreOfStickiestFalseMatch;


#define copySinglePrimerField( fieldName ) \
pPrimer->fieldName = shortPrimer.fieldName


void copyPrimerMatchesFromShorterToLongerPrimers(  
                                 primerType* pPrimerArray, 
                                 const int nNumberOfPrimers,    
                                 const bool  bForwardNotReversePrimer
                                                   ) {

   // sort primers by their 3' end so primers with the same 3' end
   // can have false and vector match information copied from 
   // shorter to longer

   // reverse primers actually end at pPrimer->nUnpaddedStart_ so
   // to sort them by their 3' end (in preparation for copying the
   // false match and vector matches), sort them by the start position

 
   if ( bForwardNotReversePrimer )
      sortPrimersByEndPosition( pPrimerArray, nNumberOfPrimers );
   else
      sortPrimersByStartPosition( pPrimerArray, nNumberOfPrimers );


   

   primerType shortPrimer;
   shortPrimer.nUnpaddedEnd_ = -1000;  // something absurd

   for( int nPrimer = 0; nPrimer < nNumberOfPrimers; ++nPrimer ) {

      primerType* pPrimer = pPrimerArray + nPrimer;


      if ( pPrimer->nUnpaddedLength_ == 
           consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_ ) {
         
         shortPrimer = *pPrimer;
      }
      else {
         if (bForwardNotReversePrimer ) {
            assert( pPrimer->nUnpaddedEnd_ == shortPrimer.nUnpaddedEnd_ );
         }
         else {
            assert( pPrimer->nUnpaddedStart_ == shortPrimer.nUnpaddedStart_ );
         }
         
         // fixed bug.  Used to copy bAcceptable_ no matter what.
         // But the problem is that a longer primer could be 
         // unacceptable due to overlapping a high quality discrepancy
         // while the shorter primer is acceptable.  Do not make 
         // an unacceptable primer be acceptable!

         if ( pPrimer->bAcceptable_ ) {
            copySinglePrimerField( bAcceptable_ );
            copySinglePrimerField( nWhyIsPrimerNotAcceptable_ );
         }

         copySinglePrimerField( nScoreOfStickiestFalseMatch_ );
         copySinglePrimerField( pContigOfStickiestFalseMatch_ );
         copySinglePrimerField( nUnpaddedOfStickiestFalseMatch_ );
         copySinglePrimerField( bContigOfStickiestFalseMatchIsComplemented_ );
         copySinglePrimerField( nSequenceInFileStickiestScore_ );
         copySinglePrimerField( nSequenceInFileSequenceNumber_ );
         copySinglePrimerField( nSequenceInFileBasePosition_ );
         copySinglePrimerField( bSequenceInFileIsComplemented_ );
      }

   }
}