/*****************************************************************************
#   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    "nAmbiguityCodeToNumber2.h"
#include    "assert.h"
#include    <ctype.h>

// here is the declaration (definition is in nAmbiguityCodeToNumber2.h)
int nAmbiguityCodeToNumber2[ nAmbiguityCodeToNumber2TableSize ];
char cAmbiguityCodeFromNumber2[ nAmbiguityCodeFromNumber2TableSize ];



void setAmbiguityCodeTables() {

   const int nA = 1;
   const int nC = 2;
   const int nG = 4;
   const int nT = 8;
   const int nGap = 16;

   int n;
   for( n = 0; n < nAmbiguityCodeToNumber2TableSize; ++n ) {
      nAmbiguityCodeToNumber2[n] = 0;
   }
   for( n = 0; n < nAmbiguityCodeFromNumber2TableSize; ++n ) {
      cAmbiguityCodeFromNumber2[n] = 0;
   }


   nAmbiguityCodeToNumber2['A'] = nA;
   nAmbiguityCodeToNumber2['C'] = nC;
   nAmbiguityCodeToNumber2['G'] = nG;
   nAmbiguityCodeToNumber2['T'] = nT;
   nAmbiguityCodeToNumber2['-'] = nGap;
   nAmbiguityCodeToNumber2['*'] = nGap;


   nAmbiguityCodeToNumber2['R'] = nA + nG;
   nAmbiguityCodeToNumber2['Y'] = nC + nT;
   nAmbiguityCodeToNumber2['W'] = nA + nT;
   nAmbiguityCodeToNumber2['S'] = nC + nG;
   nAmbiguityCodeToNumber2['M'] = nA + nC;
   nAmbiguityCodeToNumber2['K'] = nG + nT;

   nAmbiguityCodeToNumber2['B'] = nC + nG + nT;
   nAmbiguityCodeToNumber2['D'] = nA + nG + nT;
   nAmbiguityCodeToNumber2['H'] = nA + nC + nT;
   nAmbiguityCodeToNumber2['V'] = nA + nC + nG;

   nAmbiguityCodeToNumber2['E'] = nA + nGap;
   nAmbiguityCodeToNumber2['F'] = nC + nGap;
   nAmbiguityCodeToNumber2['I'] = nG + nGap;
   nAmbiguityCodeToNumber2['J'] = nT + nGap;

   nAmbiguityCodeToNumber2['N'] = nA + nC + nG + nT + nGap;


   for( n = 'a'; n <= 'z'; ++n ) {
      int nUpper = toupper( n );
      nAmbiguityCodeToNumber2[n] = nAmbiguityCodeToNumber2[nUpper];
   }


   for( n = 0; n < nAmbiguityCodeToNumber2TableSize; ++n ) {

      int nNumber = nAmbiguityCodeToNumber2[n];

      assert( nNumber < nAmbiguityCodeFromNumber2TableSize );
      
      cAmbiguityCodeFromNumber2[ nNumber ] = n;
   }
}