/*****************************************************************************
#   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_part9


   if ( bCreateSocketToControlConsed ) {
       if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
           ) {
          cerr << "-socket cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-socket must only be used with: " << endl;
          cerr << "   graphical_consed" << endl;
          exit( -1 );
       }
   }
   if ( bDoExperiments ) {
       if ( ( nWhatIsRunning != nAutoFinishIsRunning )
           ) {
          cerr << "-doExperiments cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-doExperiments must only be used with: " << endl;
          cerr << "   -autoFinish" << endl;
          exit( -1 );
       }
   }
   if ( bJustCheckAutoFinishReads ) {
       if ( ( nWhatIsRunning != nAutoFinishIsRunning )
           ) {
          cerr << "-justCheckAutoFinishReads cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-justCheckAutoFinishReads must only be used with: " << endl;
          cerr << "   -autoFinish" << endl;
          exit( -1 );
       }
   }
   if ( bID ) {
       if ( ( nWhatIsRunning != nAutoFinishIsRunning )
           ) {
          cerr << "-id cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-id must only be used with: " << endl;
          cerr << "   -autoFinish" << endl;
          exit( -1 );
       }
   }
   if ( bContigSpecified ) {
       if ( ( nWhatIsRunning != nAutoFinishIsRunning )
           ) {
          cerr << "-contig cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-contig must only be used with: " << endl;
          cerr << "   -autoFinish" << endl;
          exit( -1 );
       }
   }
   if ( bFileNamesFile ) {
       if ( ( nWhatIsRunning != nAutoFinishIsRunning )
           ) {
          cerr << "-fileNamesFile cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-fileNamesFile must only be used with: " << endl;
          cerr << "   -autoFinish" << endl;
          exit( -1 );
       }
   }
   if ( bChem ) {
       if ( ( nWhatIsRunning != nAddReadsIsRunning )
           ) {
          cerr << "-chem cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-chem must only be used with: " << endl;
          cerr << "   -addReads" << endl;
          exit( -1 );
       }
   }
   if ( bNewAceFileName ) {
       if ( ( nWhatIsRunning != nAutoEditIsRunning )
       && ( nWhatIsRunning != nAddAlignedSequenceIsRunning )
       && ( nWhatIsRunning != nTagSNPsIsRunning )
       && ( nWhatIsRunning != nAddReadsIsRunning )
       && ( nWhatIsRunning != nAddNewReadsIsRunning )
       && ( nWhatIsRunning != nRemoveReadsIsRunning )
       && ( nWhatIsRunning != nRemoveContigsIsRunning )
       && ( nWhatIsRunning != nChangeConsensusIsRunning )
           ) {
          cerr << "-newAceFileName cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-newAceFileName must only be used with: " << endl;
          cerr << "   -autoEdit" << endl;
          cerr << "   -addAlignedSequence" << endl;
          cerr << "   -tagSNPs" << endl;
          cerr << "   -addReads" << endl;
          cerr << "   -addNewReads" << endl;
          cerr << "   -removeReads" << endl;
          cerr << "   -removeContigs" << endl;
          cerr << "   -changeConsensus" << endl;
          exit( -1 );
       }
   }
   if ( bPhdWithWRItem ) {
       if ( ( nWhatIsRunning != nAddAlignedSequenceIsRunning )
           ) {
          cerr << "-phdWithWRItem cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-phdWithWRItem must only be used with: " << endl;
          cerr << "   -addAlignedSequence" << endl;
          exit( -1 );
       }
   }
   if ( bCustomNavigation ) {
       if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
           ) {
          cerr << "-nav cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-nav must only be used with: " << endl;
          cerr << "   graphical_consed" << endl;
          exit( -1 );
       }
   }
   if ( bMainContigPos ) {
       if ( ( nWhatIsRunning != nGraphicalConsedIsRunning )
           ) {
          cerr << "-mainContigPos cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-mainContigPos must only be used with: " << endl;
          cerr << "   graphical_consed" << endl;
          exit( -1 );
       }
   }
   if ( bNewPhdBallFOF ) {
       if ( ( nWhatIsRunning != nSolexa2PhdBallIsRunning )
       && ( nWhatIsRunning != nSff2PhdBallIsRunning )
       && ( nWhatIsRunning != nPhaster2PhdBallIsRunning )
           ) {
          cerr << "-phdBallFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-phdBallFOF must only be used with: " << endl;
          cerr << "   -solexa2PhdBall" << endl;
          cerr << "   -sff2PhdBall" << endl;
          cerr << "   -phaster2PhdBall" << endl;
          exit( -1 );
       }
   }
   if ( bAlignments ) {
       if ( ( nWhatIsRunning != nSelectRegionsIsRunning )
           ) {
          cerr << "-alignments cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-alignments must only be used with: " << endl;
          cerr << "   -selectRegions" << endl;
          exit( -1 );
       }
   }
   if ( bFasta ) {
       if ( ( nWhatIsRunning != nPhdBall2FastaIsRunning )
           ) {
          cerr << "-fasta cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-fasta must only be used with: " << endl;
          cerr << "   -phdBall2Fasta" << endl;
          exit( -1 );
       }
   }
   if ( bFastq ) {
       if ( ( nWhatIsRunning != nPhdBall2FastaIsRunning )
           ) {
          cerr << "-fastq cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-fastq must only be used with: " << endl;
          cerr << "   -phdBall2Fasta" << endl;
          exit( -1 );
       }
   }
   if ( bPhdBall ) {
       if ( ( nWhatIsRunning != nSff2PhdBallIsRunning )
           ) {
          cerr << "-phdBall cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-phdBall must only be used with: " << endl;
          cerr << "   -sff2PhdBall" << endl;
          exit( -1 );
       }
   }
   if ( bFOF ) {
       if ( ( nWhatIsRunning != nSff2PhdBallIsRunning )
           ) {
          cerr << "-fof cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-fof must only be used with: " << endl;
          cerr << "   -sff2PhdBall" << endl;
          exit( -1 );
       }
   }
   if ( bGenome ) {
       if ( ( nWhatIsRunning != nSnpGenomeIsRunning )
           ) {
          cerr << "-genome cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-genome must only be used with: " << endl;
          cerr << "   -snpGenome" << endl;
          exit( -1 );
       }
   }
   if ( bValid ) {
       if ( ( nWhatIsRunning != nSnpGenomeIsRunning )
           ) {
          cerr << "-valid cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-valid must only be used with: " << endl;
          cerr << "   -snpGenome" << endl;
          exit( -1 );
       }
   }
   if ( bControlFile ) {
       if ( ( nWhatIsRunning != nAddFlowcellsIsRunning )
           ) {
          cerr << "-controlFile cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-controlFile must only be used with: " << endl;
          cerr << "   -addFlowcells" << endl;
          exit( -1 );
       }
   }
   if ( bContigEndsFOF ) {
       if ( ( nWhatIsRunning != nFixContigEndsIsRunning )
           ) {
          cerr << "-contigEndsFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-contigEndsFOF must only be used with: " << endl;
          cerr << "   -fixContigEnds" << endl;
          exit( -1 );
       }
   }
   if ( bChromosomesFOF ) {
       if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
           ) {
          cerr << "-chromosomesFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-chromosomesFOF must only be used with: " << endl;
          cerr << "   -geneClassifications" << endl;
          exit( -1 );
       }
   }
   if ( bKnownGene ) {
       if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
           ) {
          cerr << "-knownGene cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-knownGene must only be used with: " << endl;
          cerr << "   -geneClassifications" << endl;
          exit( -1 );
       }
   }
   if ( bPhasterLocations ) {
       if ( ( nWhatIsRunning != nPhaster2PhdBallIsRunning )
           ) {
          cerr << "-phasterLocations cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-phasterLocations must only be used with: " << endl;
          cerr << "   -phaster2PhdBall" << endl;
          exit( -1 );
       }
   }
   if ( bPhyloFOF ) {
       if ( ( nWhatIsRunning != nGeneClassificationsIsRunning )
           ) {
          cerr << "-phyloFOF cannot be used with " << aszWhatIsRunning[ nWhatIsRunning ] << endl;
          cerr << "-phyloFOF must only be used with: " << endl;
          cerr << "   -geneClassifications" << endl;
          exit( -1 );
       }
   }