/*****************************************************************************
#   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    "contig.h"
#include    "primerType.h"
#include    "consedParameters.h"
#include    "numutil.h"
#include    <cstdlib>  // for malloc
using namespace std;
#include    "createPrimerCandidatesWith3PrimeEnd.h"
#include    "createPrimerCandidate.h"

static primerType* pPrimerArray = NULL;
static int  nNumberOfPrimersThatWillFitInPrimerArray = 0;

void   createPrimerCandidatesWith3PrimeEnd( 
                               Contig* pContig,
                               const int nUnpaddedPosOf3PrimeEnd,
                               const bool bForwardNotReversePrimer,
                               primerType*& pPrimerArrayToReturn,
                               int& nNumberOfPrimers,
                               bool& bSomeAcceptablePrimers ) {

   bSomeAcceptablePrimers = false;
   nNumberOfPrimers = 0; // will be changed as add primers

   int nMaxNumberOfPrimers = 
      consedParameters::pGetConsedParameters()->nPrimersMaximumLengthOfAPrimerToUse_ -
      consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_
      
      + 1;


   // this memory is used over and over again.  If we ultimately
   // decide to use this primer for an experiment, then
   // Contig::createExperimentWithCustomPrimer will malloc some
   // additional memory and copy this primer into it.


   if ( nMaxNumberOfPrimers > nNumberOfPrimersThatWillFitInPrimerArray ) {
      free( (char*) pPrimerArray );
      pPrimerArray = (primerType*) malloc( sizeof( primerType ) 
                                      * nMaxNumberOfPrimers );
      
      assert( pPrimerArray );
      nNumberOfPrimersThatWillFitInPrimerArray = nMaxNumberOfPrimers;
   }

   pPrimerArrayToReturn = pPrimerArray;
   
   assert( pPrimerArrayToReturn );


   if (bForwardNotReversePrimer ) {

      // nLeftEndMin
      // 
      // v
      // pppppppppppp
      //  ppppppppppp
      //   pppppppppp
      //    ppppppppp
      //    ^
      //    nLeftEndMax


      int nLeftEndMin = nUnpaddedPosOf3PrimeEnd -
         consedParameters::pGetConsedParameters()->nPrimersMaximumLengthOfAPrimerToUse_
         + 1;

      int nLeftEndMax = nUnpaddedPosOf3PrimeEnd -
          consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_
         + 1;

      int nRightEnd = nUnpaddedPosOf3PrimeEnd;

      // now prevent trying any primers that go off the left end of the
      // contig
      
      // a long primer going off the end is ok
      // ppppppppppp (ok, just truncate primer)
      //     cccccccccccccccccccccccccccccccccccc

      // but if the shortest goes over, something is wrong:
      //    pppppppp
      //     cccccccccccccccccccccccccccccccccccc
      

      int nLeftEndOfContig = pContig->nGetUnpaddedStartIndex();

      if ( nLeftEndMax < nLeftEndOfContig ) {
         cout << "nLeftEndMax < nLeftEndOfContig " << nLeftEndMax <<
            " " << nLeftEndOfContig << endl;
         assert( false );  // should have been caught before
      }

      if ( nLeftEndMin < nLeftEndOfContig )
         nLeftEndMin = nLeftEndOfContig;


      for( int nLeftEnd = nLeftEndMin; nLeftEnd <= nLeftEndMax; ++nLeftEnd ) {
         int nPrimersSoFar = nLeftEnd - nLeftEndMin;

         primerType* pPrimer = pPrimerArray + nPrimersSoFar;

         int nLengthOfPrimer = nRightEnd - nLeftEnd + 1;

         createPrimerCandidate( pPrimer, 
                                nLeftEnd, 
                                nLengthOfPrimer,
                                bForwardNotReversePrimer,
                                pContig,
                                0 ); // not important in this case

         ++nNumberOfPrimers;

         if ( pPrimer->bAcceptable_ )
            bSomeAcceptablePrimers = true;

      }
   }
   else {
      int nLeftEnd = nUnpaddedPosOf3PrimeEnd;
      int nRightEndMin = nUnpaddedPosOf3PrimeEnd +
 consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_
         - 1;
      
      int nRightEndMax = nUnpaddedPosOf3PrimeEnd +
 consedParameters::pGetConsedParameters()->nPrimersMaximumLengthOfAPrimerToUse_
         - 1;


      // Now prevent trying any primers that go off the end of the contig

      int nRightEndOfContig = pContig->nGetUnpaddedEndIndex();
      
      if ( nRightEndMin > nRightEndOfContig )
          assert( false );  // shouldn't have gotten here

      if ( nRightEndMax > nRightEndOfContig )
         nRightEndMax = nRightEndOfContig;

      

      for( int nRightEnd = nRightEndMin; nRightEnd <= nRightEndMax; ++nRightEnd ) {
         int nPrimersSoFar = nRightEnd - nRightEndMin;
         primerType* pPrimer = pPrimerArray + nPrimersSoFar;

         int nLengthOfPrimer = nRightEnd - nLeftEnd + 1;

         createPrimerCandidate( pPrimer,
                                nLeftEnd,
                                nLengthOfPrimer,
                                bForwardNotReversePrimer,
                                pContig,
                                0 );  // not important in this case

         ++nNumberOfPrimers;

         if ( pPrimer->bAcceptable_ )
            bSomeAcceptablePrimers = true;
      }
   }
}