/*****************************************************************************
#   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    "findPrimerMatchesElsewhere.h"
#include    "consedParameters.h"
#include    "contig.h"
#include    "setPrimerFalseMatchScoreArray.h"
#include    "lookForFalsePrimerMatchesOfOnePrimerInOneContig.h"
#include    "consed.h"
#include    "assembly.h"



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

   
   // don't check all primers since if the smallest match, use those
   // statistics for the longer primers that end in the same location

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

      primerType* pPrimer = pPrimerArray + nPrimer;

      if ( pPrimer->nUnpaddedLength_ !=
           consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_ ) 
         continue; 


      // the primer could already be determined to be unacceptable
      // due to poor quality
      if ( !pPrimer->bAcceptable_ ) continue;

      // set to something absurd
      pPrimer->nScoreOfStickiestFalseMatch_ = 0;
      pPrimer->pContigOfStickiestFalseMatch_ = 0;
      pPrimer->nUnpaddedOfStickiestFalseMatch_ = -10000;


      if (bCloneNotSubcloneTemplate ) {

         Assembly* pAssembly = ConsEd::pGetAssembly();

         for( int nContig = 0; nContig < pAssembly->nNumContigs(); ++nContig ) {
            Contig* pContig =  pAssembly->pGetContig( nContig );

            setPrimerFalseMatchScoreArray( pPrimer );

            lookForFalsePrimerMatchesOfOnePrimerInOneContig( 
                                            pPrimer,
                                            pContig,
                                            true, // look everywhere
                                            0,
                                            0,
                                            bForwardNotReversePrimer );

         }
      }
      else {
         // so don't look everywhere in every contig


         // in future, this may not always be true--we may want to compare
         // the primer against the ends of all contigs

         Contig* pContigOfTarget = pPrimer->pContig_;
   

         int nUnpaddedConsPosOfTargetStart = pPrimer->nUnpaddedStart_ -
   consedParameters::pGetConsedParameters()->nPrimersMaxInsertSizeOfASubclone_;

         int nUnpaddedConsPosOfTargetEnd = pPrimer->nUnpaddedStart_ +
   consedParameters::pGetConsedParameters()->nPrimersMaxInsertSizeOfASubclone_;
         
         bool bNeedToCompareToEndsOfOtherContigs = false;
         if ( nUnpaddedConsPosOfTargetStart < 
              pContigOfTarget->nGetUnpaddedStartIndex() ) {
            nUnpaddedConsPosOfTargetStart = 
               pContigOfTarget->nGetUnpaddedStartIndex();
            bNeedToCompareToEndsOfOtherContigs = true;
         }
         
         if ( nUnpaddedConsPosOfTargetEnd > 
              pContigOfTarget->nGetUnpaddedEndIndex() ) {
            nUnpaddedConsPosOfTargetEnd = 
               pContigOfTarget->nGetUnpaddedEndIndex();
            bNeedToCompareToEndsOfOtherContigs = true;
         }
         
         
         setPrimerFalseMatchScoreArray( pPrimer );
         
         lookForFalsePrimerMatchesOfOnePrimerInOneContig( 
                                               pPrimer,
                                               pContigOfTarget,
                                               false, // look everywhere
                                               nUnpaddedConsPosOfTargetStart,
                                               nUnpaddedConsPosOfTargetEnd,
                                               bForwardNotReversePrimer );
         
      } //  if (bCloneNotSubcloneTemplate )  else
      
   }
}