/*****************************************************************************
#   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    "rwcstring.h"
#include    "nGetReadTypeFromReadName.h"
#include    "readTypes.h"


int nGetReadTypeFromReadName( const RWCString& soSequenceName ) {

   // note that the default assumption is that a read is a universal primer
   // forward.
   // If there is no information in the phd file, all reads will be considered
   // universal primer reads--none walking.


   int nLastDot = soSequenceName.last( '.');
   if ( ( nLastDot == RW_NPOS ) || 
        ( nLastDot == ( soSequenceName.length() - 1 ) )  ) {
      // best guess when there is no dot in the filename or
      // when the dot is on the end
      return( nUniversalForward );
   }
   
   char cFirstCharOfExtension = soSequenceName[ nLastDot + 1 ];
   
   if ( cFirstCharOfExtension == 'r' || cFirstCharOfExtension == 'y' ||
        cFirstCharOfExtension == 'g' ) {
      // set this up so don't have to do the parsing next time
      return( nUniversalReverse );
   }
   else {
      return( nUniversalForward );
   }
}