/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef BISABASE_INCLUDED
#define BISABASE_INCLUDED


// checks that all characters are digits
// If the string is empty, returns true.
bool bIsABase( const RWCString& soString, const bool bAllowAmbiguityCodes ) {
   if (soString.length() != 1 ) return( false );

   int n = soString[0];
   int nU = toupper( n );

   if (nU == 'A' || nU == 'C' || nU == 'G' || nU == 'T' ||
       nU == 'X' || nU == 'N' || nU == '*') 
     return( true );
   else if ( bAllowAmbiguityCodes && 
             ( nU == 'R' ||
               nU == 'Y' ||
               nU == 'M' ||
               nU == 'K' ||
               nU == 'S' ||
               nU == 'W' ||
               nU == 'D' ||
               nU == 'H' ||
               nU == 'B' ||
               nU == 'V' ) )
      return( true );
   else
     return( false );
}

#endif