/*****************************************************************************
#   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.
#
#*****************************************************************************/
#define DEFINE_MATCH_MATRIX

#include    "setMatchMatrix.h"
#include    "bool.h"

//static bool bSetMatchMatrix = false;


void setMatchMatrix( const int nMatchBoost,
                     const int nMismatchPenalty ) {

   int nRow;
   int nCol;

   // I'm worried that in the future, we may have different
   // calls of this that would use different values of nMatchBoost and
   // nMismatchPenalty
   //   if ( bSetMatchMatrix ) return;
   // bSetMatchMatrix = true;

   for( nRow = 0; nRow < 256; ++nRow ) {
      for( nCol = 0; nCol < 256; ++nCol ) {
         nMatchMatrix[ nRow ][ nCol ] = -nMismatchPenalty;
      }
   }

   nMatchMatrix[ 'a' ][ 'a' ] = nMatchBoost;
   nMatchMatrix[ 'c' ][ 'c' ] = nMatchBoost;
   nMatchMatrix[ 'g' ][ 'g' ] = nMatchBoost;
   nMatchMatrix[ 't' ][ 't' ] = nMatchBoost;

   nMatchMatrix[ 'A' ][ 'A' ] = nMatchBoost;
   nMatchMatrix[ 'C' ][ 'C' ] = nMatchBoost;
   nMatchMatrix[ 'G' ][ 'G' ] = nMatchBoost;
   nMatchMatrix[ 'T' ][ 'T' ] = nMatchBoost;


   // in addition, an 'n' matching anything should be given a 
   // score of 0--not a discrepancy and not a match
   // (added Feb 2003)

   for( int n = 0; n < 256; ++n ) {
      nMatchMatrix[ 'n' ][ n ] = 0;
      nMatchMatrix[ 'N' ][ n ] = 0;
      nMatchMatrix[ n ][ 'n' ] = 0;
      nMatchMatrix[ n ][ 'N' ] = 0;
   }
}