/*****************************************************************************
#   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    "primerType.h"
#include    "nFindScoreOfSelfMatch.h"
#include    "setPrimerFalseMatchScoreArray.h"
#include    "numutil.h"
#include    <iostream.h>
#include    "consedParameters.h"
#include    "complementSequence.h"
#include    <string.h>


void findStickiestSelfMatch( primerType* pPrimer ) {

   setPrimerFalseMatchScoreArray( pPrimer );
   char szComplementedPrimer[100];
   strncpy( szComplementedPrimer, pPrimer->szPrimer_, pPrimer->nUnpaddedLength_ );

   complementSequence( szComplementedPrimer, pPrimer->nUnpaddedLength_ );

   // The reason the primer sequence is complemented is so we can look
   // for a match by looking for *equality* rather than having to look
   // for complementarity:

   //    ACGTTTCCG (3')
   // will it stick to this?
   //    GCCTTTGCA (5')   (which is the same primer just turn around.

   // To find out, complement it:

   //    CGGGAAACGT
   // and see if it match anywhere.
   

   // slide a complemented and reversed primer by an uncomplemented
   // primer and check for matches.  Slide it starting with the
   // complemented one to that it overlaps by only one base at its 3'
   // end.  Then slide with increasing more overlap and then
   // decreasing overlap until the complemented primer overlaps by
   // only 1 base at the 5' end.  and moving the complemented primer
   // to the right.  Stop when the first base of the complemented
   // primer aligns with the right-most base of the uncomplemented
   // primer.

   for( int nCompPrimerStart = -pPrimer->nUnpaddedLength_ + 1;
        nCompPrimerStart <= pPrimer->nUnpaddedLength_ - 1;
        ++nCompPrimerStart ) {
      
      int nCompPrimerEnd = nCompPrimerStart + pPrimer->nUnpaddedLength_ - 1;

      int nOverlapStart = MAX( nCompPrimerStart, 0 );

      int nOverlapEnd;
      int nUncovered3PrimeBases;
      if ( nCompPrimerEnd < pPrimer->nUnpaddedLength_ - 1 ) {
         nOverlapEnd = nCompPrimerEnd;
         nUncovered3PrimeBases = pPrimer->nUnpaddedLength_ - 1 - nCompPrimerEnd;
      }
      else {
         nOverlapEnd = pPrimer->nUnpaddedLength_ - 1;
         nUncovered3PrimeBases = 0;
      }


      int nPosOfStickiest3PrimeSubOligo = -1;
      int nScoreOfMatch = nFindScoreOfSelfMatch( 
                                      nOverlapStart, 
                                      nOverlapEnd,
                                      nUncovered3PrimeBases,
                                      szComplementedPrimer,
                                      nCompPrimerStart,
                                      nPosOfStickiest3PrimeSubOligo
                                                 );

      if (nScoreOfMatch > pPrimer->nSelfMatchScore_ ) {
         pPrimer->nSelfMatchScore_ = nScoreOfMatch;
         pPrimer->nSelfMatchOffsetOfComplementedPrimer_ =
            nCompPrimerStart;
         pPrimer->nSelfMatchPosOf3PrimeSubOligo_ =
            nPosOfStickiest3PrimeSubOligo;
      }

   }

}