/*****************************************************************************
#   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    "cGetProtein.h"
#include    <ctype.h>


char cGetProtein( const char c1,
                  const char c2,
                  const char c3 ) {

   char cU1 = tolower( c1 );
   char cU2 = tolower( c2 );
   char cU3 = tolower( c3 );


   // the isalpha allows for n to be allowed in the 3rd codon position and
   // the aa to be translated, but
   // if * or - is in the 3rd codon position, the aa is "?"

   char cProtein = '?';

   if ( cU1 == 'a' ) {
      if ( cU2 == 'a' ) {
         if ( cU3 == 'a' || cU3 == 'g' )
            cProtein = 'K';
         else if ( cU3 == 'c' || cU3 == 't' )
            cProtein = 'N';
      }
      else if ( cU2 == 'c' ) {
         if ( isalpha( cU3 ) )
            cProtein = 'T';
      }
      else if ( cU2 == 'g' ) {
         if ( cU3 == 'a' || cU3 == 'g' ) 
            cProtein = 'R';
         else if ( cU3 == 'c' || cU3 == 't' )
            cProtein = 'S';
      }
      else if ( cU2 == 't' ) {
         if ( cU3 == 'a' || cU3 == 'c' || cU3 == 't' ) 
            cProtein = 'I';
         else if ( cU3 == 'g' )
            cProtein = 'M';
      }
   }
   else if ( cU1 == 'c' ) {
      if ( cU2 == 'a' ) {
         if ( cU3 == 'a' || cU3 == 'g' ) 
            cProtein = 'Q';
         else if ( cU3 == 'c' || cU3 == 't' )
            cProtein = 'H';
      }
      else if ( cU2 == 'c' ) {
         //         if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
              cProtein = 'P';
      }
      else if ( cU2 == 'g' ) {
         //         if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
              cProtein = 'R';
      }
      else if ( cU2 == 't' ) {
         // if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
            cProtein = 'L';
      }
   }
   else if ( cU1 == 'g' ) {
      if ( cU2 == 'a' ) {
         if ( cU3 == 'a' || cU3 == 'g' ) 
            cProtein = 'E';
         else if ( cU3 == 'c' || cU3 == 't' ) 
            cProtein = 'D';
      }
      else if ( cU2 == 'c' ) {
         //         if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
            cProtein = 'A';
      }
      else if ( cU2 == 'g' ) {
         // if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
            cProtein = 'G';
      }
      else if ( cU2 == 't' ) {
         // if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
            cProtein = 'V';
      }
   }
   else if ( cU1 == 't' ) {
      if ( cU2 == 'a' ) {
         if ( cU3 == 'a' || cU3 == 'g' ) 
            cProtein = '*';
         else if  ( cU3 == 'c' || cU3 == 't' ) 
            cProtein = 'Y';
      }
      else if ( cU2 == 'c' ) {
         // if ( cU3 == 'a' || cU3 == 'g' || cU3 == 'c' || cU3 == 't' )
         if ( isalpha( cU3 ) )
            cProtein = 'S';
      }
      else if ( cU2 == 'g' ) {
         if ( cU3 == 'a' )
            cProtein = '*';
         else if ( cU3 == 'c' || cU3 == 't' ) 
            cProtein = 'C';
         else if ( cU3 == 'g' )
            cProtein = 'W';
      }
      else if ( cU2 == 't' ) {
         if ( cU3 == 'a' || cU3 == 'g' ) 
            cProtein = 'L';
         else if  ( cU3 == 'c' || cU3 == 't' ) 
            cProtein = 'F';
      }

   }      

   return( cProtein );
}