/*****************************************************************************
#   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    "printSingleSignal.h"
#include    "bIsNumericMaybeWithWhitespace.h"
#include    <stdio.h>
#include    "consedParameters.h"
#include    "consed.h"
#include    "listOfLibraries.h"
#include    "assembly.h"
#include    "contig.h"
#include    "terminateIfNoPhdDir.h"
#include    "fileDefines.h"


printSingleSignal :: printSingleSignal( const FileName& filAceFileToOpen,   
                                        const RWCString& soUnpaddedConsPos ) :
   filAceFileToOpen_( filAceFileToOpen ),   
   soUnpaddedConsPos_( soUnpaddedConsPos ) {}


void printSingleSignal :: doIt() {

   int nUnpadded;

   if ( !bIsNumericMaybeWithWhitespace( soUnpaddedConsPos_, nUnpadded ) ) {
      fprintf( stderr, "error: %s is not numeric--should be the unpadded cons pos\n",
               soUnpaddedConsPos_.data() );
      exit(1);
   }


   pCP->bOKToUseGui_ = false;

   ConsEd* pConsed = new ConsEd();

   pFILE = stdout;

    // this uses the output file to report the error
   // so it must have openAutoFinishOutputFile before it
   terminateIfNoPhdDir();

    // I want to read the list of libraries before reading the ace file
   // to make debugging by the user easier
   pCP->pListOfLibraries_ = new listOfLibraries();
   pCP->pListOfLibraries_->aLibraries_.soName_ = 
      "pCP->pListOfLibraries_->aLibraries_ in autoEdit.cpp";


   cerr << "about to parse library file" << endl;


   pCP->pListOfLibraries_->parseLibraryFile();

   cerr << "about to open ace file" << endl;

    // this does "new Assembly"
   ConsEd::pGetConsEd()->openAssemblyFile( filAceFileToOpen_ );


   Assembly* pAssembly = ConsEd::pGetAssembly();

   pAssembly->setAllPaddedPositionsArrays();

   for( int nContig = 0; nContig < pAssembly->nNumContigs(); ++nContig ) {
      Contig* pContig = pAssembly->pGetContig( nContig );

      if ( pContig->nGetUnpaddedStartIndex() <= nUnpadded &&
           nUnpadded <= pContig->nGetUnpaddedEndIndex() ) {

         pContig->printSingleSignalBases( nUnpadded );
      }
   }
}