/*****************************************************************************
#   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.
#
#*****************************************************************************/
//
// editChangeToNs.h
//
// The editChangeToNs object makes the selected portion of 
// a read low quality and changes all the bases to N's
//

#ifndef EDITCHANGETONS_INCLUDED
#define EDITCHANGETONS_INCLUDED


#include "sysdepend.h"
#include "assert.h"
#include "editActionChangeRead.h"
#include "ntide.h"
#include "locatedFragment.h"
#include    "assembly.h"



class editChangeToNs : public editActionChangeRead {

 public:

   editChangeToNs( LocatedFragment* pLocatedFragment, 
                  const int nMinConsensusPosition,
                  const int nMaxConsensusPosition )
      :
      editActionChangeRead( pLocatedFragment ),
      nMinConsensusPosition_( nMinConsensusPosition ),
      nMaxConsensusPosition_( nMaxConsensusPosition ) {}
   
   ~editChangeToNs() {}

   void doEditSpecific() {
      assert(pLocatedFragment_);  // bug spray
      
              // save old tags
      aOldTags_ = pLocatedFragment_->aTags_;

      // save the old Ntides
      for( int nCons = nMinConsensusPosition_; nCons <= nMaxConsensusPosition_;
          ++nCons ) {
         daReadNtidesBeforeEdit_.append( 
                       pLocatedFragment_->ntGetFragFromConsPos( nCons )
                                        );
      }

      pLocatedFragment_->changeToNs( nMinConsensusPosition_,
                                          nMaxConsensusPosition_ );

   }

   void undoEditSpecific() { 
      for( int nCons = nMinConsensusPosition_; nCons <= nMaxConsensusPosition_;
          ++nCons ) {
         pLocatedFragment_->overstrikeNtide( nCons, 
                     daReadNtidesBeforeEdit_[ nCons - nMinConsensusPosition_ ],
                                             false
                                            );
      }

      pLocatedFragment_->aTags_ = aOldTags_ ;
   }

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

      ConsEd :: pGetConsEd()->pAssemblyGet()->writeEditToEditHistoryFile( 
            "changeToNs %s %s %d %d", 
            (char*)pContig->soGetName().data(),
            (char*)pLocatedFragment_->soGetFragmentName().data(),
            nMinConsensusPosition_, 
            nMaxConsensusPosition_ );
   }

   virtual RWCString soGetDescriptionOfEdit() {

      Contig* pContig = pLocatedFragment_->pGetContig();

      int nMinPos = pContig->nUnpaddedIndex( nMinConsensusPosition_ );
      char szMinPos[100];
      sprintf( szMinPos, "%d", nMinPos );

      int nMaxPos = pContig->nUnpaddedIndex( nMaxConsensusPosition_ );
      char szMaxPos[100];
      sprintf( szMaxPos, "%d", nMaxPos );

      RWCString soDescription = "changeToNs " + 
         pContig->soGetName() +
         " " +
         pLocatedFragment_->soGetFragmentName() +
         " unpadded pos: " +
         szMinPos +
         " " +
         szMaxPos;

      return( soDescription );
   }

 private:
   int nMinConsensusPosition_;
   int nMaxConsensusPosition_;

   RWTValOrderedVector<Ntide> daReadNtidesBeforeEdit_;

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

};


#endif