/*****************************************************************************
#   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    "primerStickiestFalseMatch.h"
#include    "rwcstring.h"
#include    "primerType.h"
#include    "consedParameters.h"
#include    "contig.h"
#include    "abs.h"



void primerStickiestFalseMatch( primerType* pPrimer,
                               const int nPrimerNumber,
                               RWCString& soBigOutput ) {

   soBigOutput = "";
   soBigOutput.increaseMaxLength( (size_t) 2000 );

   char szDescription[500];
   
   int n5PrimeFalseMatch = 0;
   int n3PrimeFalseMatch = 0;
   RWCString soFalseMatchContigName;

   // handle case in which there is no false match at all
   // so pContigOfStickiestFalseMatch is NULL   
      

   if ( !pPrimer->pContigOfStickiestFalseMatch_ ) {
      soBigOutput.increaseMaxLengthIfNecessary( 200 );
      soBigOutput.appendFormat( 
                  "no false match.  nScoreOfStickiestFalseMatch_ = %d\n",
                  pPrimer->nScoreOfStickiestFalseMatch_ );
      return;
   }
      

   if ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) {
      n5PrimeFalseMatch = 
         pPrimer->pContigOfStickiestFalseMatch_->nComplementUnpaddedIndex( pPrimer->nUnpaddedOfStickiestFalseMatch_ );
      n3PrimeFalseMatch = n5PrimeFalseMatch -  consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_ + 1;
   }
   else {
      n5PrimeFalseMatch =
         pPrimer->nUnpaddedOfStickiestFalseMatch_;
      n3PrimeFalseMatch =
         n5PrimeFalseMatch + 
         consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_ 
         - 1;
   }

   soFalseMatchContigName = pPrimer->pContigOfStickiestFalseMatch_->soGetName();


   for( int n = 0; n < pPrimer->nUnpaddedLength_; ++n )
      soBigOutput.append( *(pPrimer->szPrimer_ + n) );


   soBigOutput.increaseMaxLengthIfNecessary( 200 );
   soBigOutput.appendFormat( "    primer: %d  match elsewhere score: %d\n", 
                             nPrimerNumber,
                             pPrimer->nScoreOfStickiestFalseMatch_ );



   // false matches are determined by examining just the suboligo of
   // length nPrimersMinimumLengthOfAPrimer_
   // This may be less than nUnpaddedLength_ of the primer.  So to
   // show the alignment, put spaces to start with

   if ( ABS( n5PrimeFalseMatch - n3PrimeFalseMatch ) + 1 <
        pPrimer->nUnpaddedLength_ ) {
      
      int nNumberOfSpacesToAdd = pPrimer->nUnpaddedLength_ -
         ABS( n5PrimeFalseMatch - n3PrimeFalseMatch ) - 1;

      for( int n = 0; n < nNumberOfSpacesToAdd; ++n )
         soBigOutput.append( ' ' );
   }


   if ( pPrimer->pContigOfStickiestFalseMatch_ ) {
      if (  pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ) {
         for( int nUnpadded = n5PrimeFalseMatch;
              nUnpadded >= n3PrimeFalseMatch;
              --nUnpadded ) {
            int nConsPos =pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded );
            char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase();
            soBigOutput.append( cComplementBase( c ) );
         }
      }
      else {
         for( int nUnpadded = n5PrimeFalseMatch;
              nUnpadded <= n3PrimeFalseMatch;
              ++nUnpadded ) {
            
            int nConsPos = pPrimer->pContigOfStickiestFalseMatch_->nPaddedIndexFast( nUnpadded );
            char c = pPrimer->pContigOfStickiestFalseMatch_->ntGetCons( nConsPos ).cGetBase();
            soBigOutput.append( c );
         }
      }

   }


   soBigOutput.increaseMaxLengthIfNecessary( 1000 );
   soBigOutput.appendFormat( "   false match at %s 5': %6d 3': %6d %s\n",
            (char*) soFalseMatchContigName.data(),
            n5PrimeFalseMatch,
            n3PrimeFalseMatch,
            ( pPrimer->bContigOfStickiestFalseMatchIsComplemented_ ?
              "Complemented" : "not complemented" )
            );

}