/*****************************************************************************
#   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.
#
#*****************************************************************************/
//
// editoverstrike.h
//
// The EditOverstrike object sets the ntide at the passed 
// consensus relative position to the new value.  This edit action
// only allows editing the read
//

#ifndef EDITOVERSTRIKE_INCLUDED
#define EDITOVERSTRIKE_INCLUDED


#ifdef SCCS_ID
static const char* editOverstrikeSccsId = "@(#)editoverstrike.h	1.10 04/01/96 15:03:30";
#endif


#include "sysdepend.h"
#include "assert.h"
#include "editaction.h"
#include "contig.h"
#include "locatedFragment.h"
#include "editActionChangeRead.h"
#include "assembly.h"
#include "contigwin.h"


class EditOverstrike : public editActionChangeRead {

 public:

   EditOverstrike(LocatedFragment* pLocatedFragment,  
                                   // if null, edit consensus
                  const int nConsPos,
                  const Ntide nt)
      :
      editActionChangeRead( pLocatedFragment ),
      nConsPos_(nConsPos),
      ntNew_(nt) {}
   
   ~EditOverstrike() {}

   virtual void doEditSpecific() {
      
      ntOld_ = pLocatedFragment_->ntGetFragFromConsPos(nConsPos_);  
              // save old
      aOldTags_ = pLocatedFragment_->aTags_;

      pLocatedFragment_->overstrikeNtide( nConsPos_, ntNew_, true);
   }

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

      int nUnpadded = pContig->nUnpaddedIndex( nConsPos_ );
      char szTemp[200];
      sprintf( szTemp, "%d", nUnpadded );
         

      RWCString soDescription = "overstrike " + pContig->soGetName() +
         " " + pLocatedFragment_->soGetFragmentName() + " unpadded pos: " +
         szTemp +
         + " old: " + 
         RWCString( ntOld_.cGetBaseUpperOrLower() ) +
         " new: " +
         RWCString( ntNew_.cGetBaseUpperOrLower() );

      return( soDescription );
   }


   void undoEditSpecific() { 

      // put the old one back.

      pLocatedFragment_->overstrikeNtide(nConsPos_, ntOld_, false);
      pLocatedFragment_->aTags_ = aOldTags_ ;
   }

  virtual void writeEditToEditHistoryFile() {
    Contig* pContig = pLocatedFragment_->pGetContig();

    ConsEd :: pGetConsEd()->pAssemblyGet()->writeEditToEditHistoryFile( 
            "overstrike %s %s %d %c", 
            (char*)pContig->soGetName().data(),
            (char*)pLocatedFragment_->soGetFragmentName().data(),
            nConsPos_, 
            ntNew_.cGetBaseUpperOrLower() );
  }

   


 private:
   // consensus relative position of ntide affected
   int nConsPos_;

   // new Ntide
   Ntide ntNew_;

   // save the old Ntide here 
   Ntide ntOld_;

   // save all old tags
   RWTPtrOrderedVector<tag> aOldTags_;

};


#endif // EDITOVERSTRIKE_INCLUDED