/*****************************************************************************
#   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    <stdio.h>
#include    "rwcstring.h"
#include    "locatedFragment.h"
#include    "rwctokenizer.h"
#include    "consedParameters.h"
#include    "guicolortext.h"
#include    "colorDefaults.h"
#include    "assembly.h"
#include    "consed.h"
#include    "guiapp.h"



void readAndProcessReadPrefixFile() {


   FILE* pReadPrefixFile = fopen( pCP->filReadPrefixesFile_.data(), "r" );

   if ( !pReadPrefixFile ) {
      cerr << "no consed.readPrefixesFile: " << pCP->filReadPrefixesFile_ << 
         " that's ok" << endl;
      return;
   }

   // the file exists!  So process it.

   Assembly* pAssembly = ConsEd::pGetAssembly();

   const int nMaxLineSize = 2000;
   RWCString soLine( (size_t) nMaxLineSize );

   while( fgets( soLine.data(), nMaxLineSize, pReadPrefixFile ) != NULL ) {

      soLine.nCurrentLength_ = strlen( soLine.data() );

      RWCTokenizer tok( soLine );

      RWCString soReadName = tok();
      RWCString soPrefix = tok();
      RWCString soColor = tok();

      // find the read:

      LocatedFragment* pLocFrag = 
         pAssembly->pGetLocatedFragmentByName( soReadName );

      if ( !pLocFrag ) {
         cerr << "Warning:  read " << soReadName << " in file " <<
            pCP->filReadPrefixesFile_ << " does not exist in assembly " << endl;
         continue;
      }

      if ( !pLocFrag->soReadPrefix_.isNull() ) {
         cerr << "Warning:  read " << soReadName << " is twice in file " <<
            pCP->filReadPrefixesFile_ << endl;
         continue;
      }


      if ( soPrefix.isNull() ) {
         pLocFrag->soReadPrefix_ = pCP->soDefaultReadPrefix_;
      }
      else {
         pLocFrag->soReadPrefix_ = soPrefix;
      }

      if ( soColor.isNull() ) {
         pLocFrag->pGctForReadPrefix_ = 
            GuiApp::pGetGuiApp()->pColorReadPrefixDefault_;
      }
      else {
         pLocFrag->pGctForReadPrefix_ = 
            GAPP->pGetGuiColorTextForReadPrefixColor( soColor );

      }
   }

   fclose( pReadPrefixFile );

}