/*****************************************************************************
#   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    "removeReads.h"
#include    "automatedConsedInit.h"
#include    "soLine.h"
#include    "guiRemoveReads.h"
#include    "consed.h"
#include    "locatedFragment.h"


void removeReads :: doIt() {

   automatedConsedInit( filAceFileToOpen_ );
   
   guiRemoveReads myGuiRemoveReads;

   readFileOfReadsToRemove( myGuiRemoveReads.aReadsToRemove_ );
   
   RWCString soMessage;
   myGuiRemoveReads.doItNoGui( pCP->bRemoveReadsDeleteNotJustPutInOwnContig_,
                               soMessage );

   cerr << soMessage << endl;

   ConsEd::pGetAssembly()->saveAssemblyToUserSpecifiedOrNextAvailableVersionOfAceFile( filNewAceFile_ );
}


void removeReads :: readFileOfReadsToRemove( 
   RWTPtrOrderedVector<LocatedFragment>& aReadsToRemove ) {

   FILE* pReadsToRemove = fopen( filReadsToBeRemoved_.data(), "r" );
   if ( !pReadsToRemove ) {
      RWCString soMessage = "file of reads to be removed: " + filReadsToBeRemoved_;
      THROW_FILE_ERROR( soMessage );
   }


   int nNumberOfReads = 0;
   while( fgets( soLine.data(), nMaxLineSize, pReadsToRemove ) != NULL ) {
      soLine.nCurrentLength_ = strlen( soLine.data() );

      // there might be leading and/or trailing whitespace
      soLine.stripAllWhitespaceExceptInternal();

      // see if we can find this read

      LocatedFragment* pLocFrag = 
         ConsEd::pGetAssembly()->pGetLocatedFragmentByName( soLine );

      if ( !pLocFrag ) {
         cerr << "couldn't find read " << soLine << endl;
         continue;
      }
      
      ++nNumberOfReads;
   }

   aReadsToRemove.resize( nNumberOfReads );


   rewind( pReadsToRemove );

   while( fgets( soLine.data(), nMaxLineSize, pReadsToRemove ) != NULL ) {
      soLine.nCurrentLength_ = strlen( soLine.data() );

      // there might be leading and/or trailing whitespace

      soLine.stripAllWhitespaceExceptInternal();


      // see if we can find this read

      LocatedFragment* pLocFrag =
         ConsEd::pGetAssembly()->pGetLocatedFragmentByName( soLine );

      if (!pLocFrag ) continue;
      
      aReadsToRemove.insert( pLocFrag );
   }

   fclose( pReadsToRemove );

}