/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef editChangeToXs_included
#define editChangeToXs_included

class editChangeToXs : public editActionChangeRead {

public:
   
   editChangeToXs( LocatedFragment* pLocatedFragment,
                   const int nLeftConsPos,
                   const int nRightConsPos,
                   const char cRightOrLeft )
      :
      editActionChangeRead( pLocatedFragment ),
      nLeftConsPos_( nLeftConsPos ),
      nRightConsPos_( nRightConsPos ),
      cRightOrLeft_( cRightOrLeft ) {}

   void doEditSpecific() {
      assert( pLocatedFragment_ );

      // save old tags

      aOldTags_ = pLocatedFragment_->aTags_;

      assert( pLocatedFragment_->nGetAlignStart() <= nLeftConsPos_ &&
              nLeftConsPos_ <= nRightConsPos_ &&
              nRightConsPos_ <= pLocatedFragment_->nGetAlignEnd() );

      // save old Ntides

      for( int nCons = nLeftConsPos_; nCons <= nRightConsPos_;
           ++nCons ) {
         daReadNtidesBeforeEdit_.append(
           pLocatedFragment_->ntGetFragFromConsPos( nCons )
                                        );
      }

      pLocatedFragment_->changeToXs( nLeftConsPos_,
                                     nRightConsPos_ );

   }


   void undoEditSpecific() {


      assert( pLocatedFragment_->nGetAlignStart() <= nLeftConsPos_ &&
              nLeftConsPos_ <= nRightConsPos_ &&
              nRightConsPos_ <= pLocatedFragment_->nGetAlignEnd() );

      // restore old Ntides

      for( int nCons = nLeftConsPos_;
           nCons <= nRightConsPos_; ++nCons ) {
         
         pLocatedFragment_->overstrikeNtide(
               nCons,
               daReadNtidesBeforeEdit_[ nCons - nLeftConsPos_ ],
               false ); // bAddEditTag
      }

      pLocatedFragment_->aTags_ = aOldTags_;
   }

   virtual void writeEditToEditHistoryFile() {
      Contig* pContig = pLocatedFragment_->pGetContig();
      
      ConsEd::pGetConsEd()->pAssemblyGet()->writeEditToEditHistoryFile(
          "%s %s %s %d",
          ( cRightOrLeft_ == 'r' ? "changeToXsToRight" : "changeToXsToLeft" ),
          pContig->soGetName().data(),
          pLocatedFragment_->soGetFragmentName().data(),
          ( cRightOrLeft_ == 'r' ? nLeftConsPos_ : nRightConsPos_ ) );
   }

   virtual RWCString soGetDescriptionOfEdit() {
      Contig* pContig = pLocatedFragment_->pGetContig();

      int nUnpadded;
      if ( cRightOrLeft_ == 'r' )
         nUnpadded = pContig->nUnpaddedIndex( nLeftConsPos_ );
      else
         nUnpadded = pContig->nUnpaddedIndex( nRightConsPos_ );

      RWCString soDescription;
      if ( cRightOrLeft_ == 'r' )
         soDescription = "change to X's to right ";
      else
         soDescription = "change to X's to left ";

      soDescription = soDescription +
         pContig->soGetName() +
         " " + pLocatedFragment_->soGetFragmentName() +
         " unpadded pos: " + RWCString( (long) nUnpadded );

      return( soDescription );
   }


private:
   int nLeftConsPos_;
   int nRightConsPos_;
   char cRightOrLeft_;

   RWTValOrderedVector<Ntide> daReadNtidesBeforeEdit_;
   
   // save all old tags
   RWTPtrOrderedVector<tag> aOldTags_;

};

#endif