/*****************************************************************************
#   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.
#
#*****************************************************************************/




// main.cpp_part6 start
   int nWhatIsRunning = nGraphicalConsedIsRunning;

   // nWhatIsRunning might be changed below--
   // nGraphicalConsedIsRunning is just the default

   for( n = 1; n < nArgc; ++n ) {
      RWCString soLowerCaseArg( argv[n] );
      soLowerCaseArg.toLower();
      if ( soLowerCaseArg % aszWhatIsRunning[ 2 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 2;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 3 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 3;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 4 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 4;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 5 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 5;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 6 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 6;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 7 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 7;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 8 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 8;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 9 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 9;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 10 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 10;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 11 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 11;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 12 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 12;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 13 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 13;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 14 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 14;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 15 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 15;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 16 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 16;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 17 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 17;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 18 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 18;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 19 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 19;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 20 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 20;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 21 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 21;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 22 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 22;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 23 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 23;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 24 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 24;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 25 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 25;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 26 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 26;
      }
      if ( soLowerCaseArg % aszWhatIsRunning[ 27 ] ) {
         // check if a group has already been assigned
         if ( nWhatIsRunning != nGraphicalConsedIsRunning ) {
            cerr << "Fatal Error: arguments " << aszWhatIsRunning[ nWhatIsRunning ] << " and " << argv[n] << " are mutually incompatible" << endl;
            exit( -1 );
         }

         nWhatIsRunning = 27;
      }
   }
   // when reached here, we know that the user has not specified running more
   // than one program and we have determined what that program is
   if ( nWhatIsRunning != nGraphicalConsedIsRunning )
      cerr << aszWhatIsRunning[ nWhatIsRunning ] << " will be run." << endl;