/*****************************************************************************
#   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    "editOverstrikeAllReadsAtConsPos.h"
#include    "locatedFragment.h"
#include    "contig.h"
#include    "consed.h"


void editOverstrikeAllReadsAtConsPos :: doEditSpecific() {


   cNewConsensusBase_ = pMasterLocFrag_->ntGetFragFromConsPos( nConsPos_ ).cGetBase();

   bool bNewNtideIsPad = ( cNewConsensusBase_ == '*' ? true : false );

   for( int nRead = 0; nRead < aArrayOfReadsToOverstrike_.length();
        ++nRead ) {

      LocatedFragment* pLocFrag = aArrayOfReadsToOverstrike_[ nRead ];

      char cOldBase = pLocFrag->ntGetFragFromConsPos( nConsPos_ ).cGetBase();
      Quality qualOld = pLocFrag->ntGetFragFromConsPos( nConsPos_ ).qualGetQuality();
      aOldBases_.insert( cOldBase );


      aOldQualities_.insert( qualOld );
      aOldTagArrays_.insert( pLocFrag->aTags_ );


      if ( cOldBase == cNewConsensusBase_ ) {
         aWasReadOverstruck_.insert( false );
         continue;
      }
      else {
         aWasReadOverstruck_.insert( true );
      }

      // if reached here, the read must be changed

      pLocFrag->makeCopyOfPhredCallsIfNecessary();

      int nFragIndex = pLocFrag->nGetFragIndexFromConsPos( nConsPos_ );

      pLocFrag->Sequence::setBaseAtPos( 
                                       nFragIndex,
                                       cNewConsensusBase_ );

      pLocFrag->setQualityAtConsPos( nConsPos_, ucQualityLowEdited );


      bool bOldNtideWasPad = ( cOldBase == '*' ? true : false );

      pLocFrag->addEditTag( bOldNtideWasPad, bNewNtideIsPad, nConsPos_ );
   }

   // and now fix the consensus

   Contig* pContig = pMasterLocFrag_->pContig_;

   cOldConsensusBase_ = pContig->ntGetCons( nConsPos_ ).cGetBase();
   qualOldConsensusQuality_ = pContig->ntGetCons( nConsPos_ ).qualGetQuality();

   pContig->Sequence::setBaseAtPos( nConsPos_, cNewConsensusBase_ );

   pContig->Sequence::setQualityAtSeqPos( nConsPos_, ucQualityLowEdited );

   // added May 2009 (DG) when noticed that when click on a base in
   // Aligned Reads Window, wrong unpadded position is displayed

   bool bOldNtideIsPad = ( cOldConsensusBase_ == '*' ? true : false );


   if ( bOldNtideIsPad != bNewNtideIsPad ) {
      pContig->setUnpaddedPositionsArray();
   }

   // end of added May 2009

}


void editOverstrikeAllReadsAtConsPos :: undoEditSpecific() {

   for( int nRead = 0; nRead < aArrayOfReadsToOverstrike_.length();
        ++nRead ) {

      LocatedFragment* pLocFrag = aArrayOfReadsToOverstrike_[ nRead ];

      char cOldBase = aOldBases_[ nRead ];
      Quality qualOld = aOldQualities_[ nRead ];

      if ( cOldBase != 
           pLocFrag->ntGetFragFromConsPos( nConsPos_ ).cGetBase() ) {

         int nFragPos = pLocFrag->nGetFragIndexFromConsPos( nConsPos_ );

         pLocFrag->Sequence::setBaseAtPos( nFragPos, cOldBase );

         pLocFrag->Sequence::setQualityAtSeqPos( nFragPos, qualOld );

         // how shall I remove the edit tag?

         pLocFrag->aTags_ = aOldTagArrays_[ nRead ];

         // and how about the phredBaseCalls?  There is no reason
         // to remove them.  They do not change.
      }
   }

   // and now reset the consensus

   Contig* pContig = pMasterLocFrag_->pContig_;
   
   pContig->Sequence::setBaseAtPos( nConsPos_, cOldConsensusBase_ );
   pContig->Sequence::setQualityAtSeqPos( nConsPos_, qualOldConsensusQuality_ );
   // added May 2009 (DG) when noticed that when click on a base in
   // Aligned Reads Window, wrong unpadded position is displayed

   bool bOldNtideIsPad = ( cOldConsensusBase_ == '*' ? true : false );
   bool bNewNtideIsPad = ( cNewConsensusBase_ == '*' ? true : false );


   if ( bOldNtideIsPad != bNewNtideIsPad ) {
      pContig->setUnpaddedPositionsArray();
   }

   // end of added May 2009

}

         
      

void editOverstrikeAllReadsAtConsPos :: writeEditToEditHistoryFile() {

   Contig* pContig = pMasterLocFrag_->pGetContig();

   RWCString soLineToWrite( (size_t) 1000 );

   soLineToWrite.nCurrentLength_ = 
      sprintf(  soLineToWrite.data(), "changeAllReads %s %s %d",
                pContig->soGetName().data(),
                pMasterLocFrag_->soGetName().data(),
                nConsPos_ );

   assert( soLineToWrite.nCurrentLength_ > 0 );

   for( int nRead = 0; nRead < aArrayOfReadsToOverstrike_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToOverstrike_[ nRead ];
      soLineToWrite += " ";
      soLineToWrite += aArrayOfReadsToOverstrike_[ nRead ]->soGetName();
   }
                

   ConsEd::pGetAssembly()->writeEditToEditHistoryFile( soLineToWrite.data() );

}


RWCString editOverstrikeAllReadsAtConsPos :: soGetDescriptionOfEdit() {

   Contig* pContig = pMasterLocFrag_->pGetContig();

   char cBase = pMasterLocFrag_->ntGetFragFromConsPos( nConsPos_ ).cGetBase();

   RWCString soDescription = "changeAllReads in " +
      pContig->soGetName() + " to match " + pMasterLocFrag_->soGetName() +
      " at " + RWCString( (long) pContig->nUnpaddedIndex( nConsPos_ ) ) +
      " which is " + RWCString( cBase );

   return( soDescription );
}


void editOverstrikeAllReadsAtConsPos :: setChangedIfNecessary() {

   Contig* pContig = pMasterLocFrag_->pContig_;
   bOldContigChanged_ = pContig->bChanged();
   bOldAssemblyChanged_ = ConsEd::pGetAssembly()->bChanged();

   for( int nRead = 0; nRead < aArrayOfReadsToOverstrike_.length();
        ++nRead ) {

      LocatedFragment* pLocFrag = aArrayOfReadsToOverstrike_[ nRead ];

      aOldReadsChanged_.insert( pLocFrag->bChanged() );

      if ( aWasReadOverstruck_[ nRead ] ) {
         pLocFrag->setChanged();
      }
   }
}
   

void editOverstrikeAllReadsAtConsPos :: undoSetChangedIfNecessary() {

   for( int nRead = 0; nRead < aArrayOfReadsToOverstrike_.length();
        ++nRead ) {

      if ( !aWasReadOverstruck_[ nRead ] )  continue;

      LocatedFragment* pLocFrag = aArrayOfReadsToOverstrike_[ nRead ];
      if ( !aOldReadsChanged_[ nRead ] ) {
         pLocFrag->setUnchanged();
      }
   }

   if ( ! bOldContigChanged_ ) {
      pMasterLocFrag_->pGetContig()->setUnchanged();
   }

   if ( ! bOldAssemblyChanged_ ) {
      ConsEd::pGetAssembly()->setUnchanged();
   }

}