/*****************************************************************************
#   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    "editMakeHighQualityAndChangeConsensus.h"
#include    "consedParameters.h"


void editMakeHighQualityAndChangeConsensus :: doEditSpecific() {

   assert ( pLocatedFragment_);

   Contig* pContig = pLocatedFragment_->pGetContig();

   assert( nMinConsensusPosition_ <= nMaxConsensusPosition_ );

   if ( nMinConsensusPosition_ < pContig->nGetStartConsensusIndex() ) {
      ostringstream ost;
      ost << 
         "You cannot extend the consensus on the left end, but you can extend it on the right end.  So complement, extend, and complement back."
          << ends;

      InputDataError ide(ost.str().c_str());
      throw ide;
   }


   bExtendingConsensus_ = false;
   if ( nMaxConsensusPosition_ > pContig->nGetEndConsensusIndex() ) {
      if ( nMinConsensusPosition_ == ( pContig->nGetEndConsensusIndex() + 1 )) {
         bExtendingConsensus_ = true;
         nOldLengthOfConsensus_ = pContig->nGetPaddedSeqLength();
      }
      else {
         ostringstream ost;
         ost << 
            "If you want to extend the consensus, you must swipe starting from the base precisly after the end of the consensus."
             << ends;

         InputDataError ide(ost.str().c_str());
         throw ide;
      }
   }



   // save old read Ntides
   int nCons;
   for ( nCons = nMinConsensusPosition_;
        nCons <= nMaxConsensusPosition_;
        nCons++) {

      daReadNtidesBeforeEdit_.append(
                                     pLocatedFragment_->ntGetFragFromConsPos( nCons )
                                     );
   }

   bool bThereArePads = false;


   if (!bExtendingConsensus_ ) {

      // save the consensus Ntides
      for ( nCons = nMinConsensusPosition_;
            nCons <= nMaxConsensusPosition_;
            nCons++) {
         // save the old value of the consensus ntide at that pos
         daConsNtidesBeforeEdit_.append(pContig->ntGetCons(nCons));
         if (pContig->ntGetCons(nCons).bIsPad() )
            bThereArePads = true;
      }
   }


      
   if ( bExtendingConsensus_ ) {

      if ( pCP->bExtendConsensusWithHighQuality_ ) {
         // make the read high quality
         pLocatedFragment_->makeHighQuality( nMinConsensusPosition_,
                                             nMaxConsensusPosition_ );
      }


      for( nCons = nMinConsensusPosition_;
           nCons <= nMaxConsensusPosition_;
           ++nCons ) {

         pContig->appendNtide( pLocatedFragment_->ntGetFragFromConsPos(nCons) );

         // this really isn't necessary since we are going to 
         // setUnpaddedPositionsArray() whenever we are extending the
         // consensus regardless whether there are pads or not

         if (pContig->ntGetCons( nCons ).bIsPad() )
            bThereArePads = true;
      }


      // extend the aligned region of the read, per request from
      // Eugene Goltsman, 2005

      if ( pLocatedFragment_->bIsWholeReadUnaligned() ) {
         pLocatedFragment_->nAlignClipStart_ = nMinConsensusPosition_;
         pLocatedFragment_->nAlignClipEnd_ = nMaxConsensusPosition_;
      }
      else {
         // this is a little dangerous--we are going to extend
         // the aligned region to be the union of the old, the new,
         // and anything in between

         int nNewAlignClipStart = MIN( pLocatedFragment_->nAlignClipStart_,
                                       nMinConsensusPosition_ );

         int nNewAlignClipEnd = MAX( pLocatedFragment_->nAlignClipEnd_,
                                     nMaxConsensusPosition_ );
         

         pLocatedFragment_->nAlignClipStart_ = nNewAlignClipStart;
         pLocatedFragment_->nAlignClipEnd_ = nNewAlignClipEnd;
      }

   }
   else {

      // make the read high quality
      pLocatedFragment_->makeHighQuality( nMinConsensusPosition_,
                                          nMaxConsensusPosition_ );


      // copy the read to the consensus
      for ( nCons = nMinConsensusPosition_;
            nCons <= nMaxConsensusPosition_;
            nCons++) {
         pContig->setNtideAtPos(nCons, 
                                pLocatedFragment_->ntGetFragFromConsPos(nCons) );
         if (pContig->ntGetCons( nCons ).bIsPad() )
            bThereArePads = true;
      }

   }

   if (bThereArePads || bExtendingConsensus_ )
      pContig->setUnpaddedPositionsArray();


   // change the base segment array
   pBaseSegChanges_ =
      pContig->baseSegArray_.setBaseSegToFragRegion(pLocatedFragment_,
                                                    nMinConsensusPosition_,
                                                    nMaxConsensusPosition_ );

}


void editMakeHighQualityAndChangeConsensus :: undoEditSpecific() { 
   // restore base segment array changes
   Contig* pContig = pLocatedFragment_->pGetContig();

   pContig->baseSegArray_.undoBaseSegChanges(pBaseSegChanges_);


   if ( bExtendingConsensus_ ) {
      int nBasesToDelete = pContig->nGetPaddedConsLength() -
         nOldLengthOfConsensus_;

      assert( nBasesToDelete > 0 );

      for( int nBases = 1; nBases <= nBasesToDelete; ++nBases ) {
         pContig->removeLastBase();
      }
   }


   // restore the consensus sequence
   for (int n = 0;
        n < daConsNtidesBeforeEdit_.length();
        n++) {
      // replace the old value of the consensus ntide at that pos
      pContig->setNtideAtPos(n+nMinConsensusPosition_,daConsNtidesBeforeEdit_[n]);
   }

   pContig->setUnpaddedPositionsArray();

      // restore old read Ntides
   for (int nCons = nMinConsensusPosition_;
        nCons <= nMaxConsensusPosition_;
        nCons++) {

      pLocatedFragment_->overstrikeNtide( nCons, 
                                          daReadNtidesBeforeEdit_[ nCons - nMinConsensusPosition_ ],
                                          false
                                          );
   }

}