/*****************************************************************************
#   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    "clScaffold.h"
#include    "contig.h"
#include    "editaction.h"
#include    "consed.h"
#include    "edit_complement_contig.h"



void clScaffold :: setScaffoldLength() {

   Contig* pLastContig = aContigs_[ aContigs_.length() - 1 ];

   nScaffoldLength_ = pLastContig->nClonePosRight_;
}


RWCString clScaffold :: soGetDescription() {

   RWCString soScaffoldMap;
   soScaffoldMap.increaseMaxLength( (size_t) ( aContigs_.length() * 5 ) );

   for( int nContig = 0; nContig < aContigs_.length(); ++nContig ) {
      Contig* pContig = aContigs_[ nContig ];

      if ( nContig == 0 ) {
         if ( pContig->bThisContigIsComplementedInTheScaffold_ ) {
            if ( pContig->bIsThisEndTheEndOfTheClone( nRightGap ) ) {
               soScaffoldMap += "E-";
            }
         }
         else {
            if ( pContig->bIsThisEndTheEndOfTheClone( nLeftGap ) ) {
               soScaffoldMap += "E-";
            }
         }
      }
      else {
         soScaffoldMap += "-";
      }


      soScaffoldMap += pContig->soGetAbbreviatedName();
      if ( pContig->bThisContigIsComplementedInTheScaffold_ )
         soScaffoldMap += "c";



      if ( nContig == ( aContigs_.length() - 1 ) ) {
         if ( pContig->bThisContigIsComplementedInTheScaffold_ ) {
            if ( pContig->bIsThisEndTheEndOfTheClone( nLeftGap ) ) {
               soScaffoldMap += "-E";
            }
         }
         else {
            if ( pContig->bIsThisEndTheEndOfTheClone( nRightGap ) ) {
               soScaffoldMap += "-E";
            }
         }
      }
   }

   return( soScaffoldMap );
}



void clScaffold :: removeTheCs() {

   
   for( int nContig = 0; nContig < aContigs_.length(); ++nContig ) {
      Contig* pContig = aContigs_[ nContig ];

      if ( pContig->bThisContigIsComplementedInTheScaffold_ ) {

         if ( nContig == 0 ) {
            if ( bUseFirstContigUnpaddedStart_ ) {
               // must changed nFirstContigUnpaddedStart_ into new coordinates

               nFirstContigUnpaddedStart_ = 
                  pContig->nComplementUnpaddedIndex( nFirstContigUnpaddedStart_ );
            }
         }

         if ( nContig ==  aContigs_.length() - 1 ) {
            if ( bUseLastContigUnpaddedEnd_ ) {
               nLastContigUnpaddedEnd_ = 
                  pContig->nComplementUnpaddedIndex( nLastContigUnpaddedEnd_ );
            }
         }


         cerr << "complementing " << pContig->soGetName() << endl;

         // complement the contig

         EditAction *pEditAction = new EditComplementContig( pContig );
         ConsEd::pGetConsEd()->doEditAction( pEditAction, 
                                             true ); // write to .wrk
      }
      else {
         cerr << "not complementing " << pContig->soGetName() << endl;
      }
   }

   // ConsEd::pGetConsEd()->refreshAllContigWinsAndAllTeditors();
}





void clScaffold :: fixOrientation( RWCString& soErrorMessage ) {

   // each contig should have a WR item added to one read indicating 
   // its position.


   for( int nContig = 0; nContig < aContigs_.length(); ++nContig ) {
      Contig* pContig = aContigs_[ nContig ];

      RWCString soErrorMessage2;
      pContig->fixOrientation( soErrorMessage2 );
      soErrorMessage += soErrorMessage2;
   }

}





void clScaffold :: flipScaffold() {

   // -1 means the scaffold is user-defined, as in the digest
   if ( nScaffold_ != -1 )
      ConsEd::pGetAssembly()->reverseScaffold( nScaffold_ );

   aContigs_.reverseElementOrder();
   aIfContigsAreComplemented_.reverseElementOrder();

   for( int nContig = 0; nContig < aIfContigsAreComplemented_.length(); 
        ++nContig ) {
      aIfContigsAreComplemented_[ nContig ] =
         !aIfContigsAreComplemented_[ nContig ];

   }

   bool bTemp;
   
   bTemp = bFirstContigIsCloneEnd_;
   bFirstContigIsCloneEnd_ = bLastContigIsCloneEnd_;
   bLastContigIsCloneEnd_ = bTemp;

   // don't know if this is necessary
   aContigEndPairs_.reverseElementOrder();
  
   bTemp = bUseFirstContigUnpaddedStart_;
   bUseFirstContigUnpaddedStart_ = bUseLastContigUnpaddedEnd_;
   bUseLastContigUnpaddedEnd_ = bTemp;

   int nTemp = nFirstContigUnpaddedStart_;
   nFirstContigUnpaddedStart_ = nLastContigUnpaddedEnd_;
   nLastContigUnpaddedEnd_ = nTemp;

   // I do not believe these positions need to be complemented.
   // For example, suppose nFirstContigUnpaddedStart_ = 1 in ContigA.
   // After flipping the scaffold, ContigA will be the last contig,
   // and will be ContigAc (complemented in the scaffold) so position 1 will
   // be the last position in the scaffold, which is what we want.  
   // We do not want to change this to 32123 (or whatever the last position
   // in that contig is).

}

 

void clScaffold :: unfixOrientation() {

   for( int nContig = 0; nContig < aContigs_.length(); ++nContig ) {
      Contig* pContig = aContigs_[ nContig ];
      pContig->unfixOrientation();
   }
}