/*****************************************************************************
#   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    "editAddTagsToAllReadsAtConsPos.h"
#include    "locatedFragment.h"
#include    "contig.h"
#include    "bIntervalsIntersect.h"
#include    "contigview.h"
#include    "tag.h"
#include    "consed.h"



void editAddTagsToAllReadsAtConsPos :: doEditSpecific() {

   // get a list of all the reads at this cons pos

   ContigView* pContigView = pContig_->pGetContigView( nConsPosLeft_,
                                                       nConsPosRight_ );

   int nRead;
   for( nRead = 0; nRead < pContigView->nGetNumberOfFragments();
        ++nRead ) {
      LocatedFragment* pLocFrag = pContigView->pLocatedFragmentGet( nRead );

      if ( pLocFrag->bIsWholeReadUnaligned() ) continue;

      if ( !bIntervalsIntersect( pLocFrag->nGetAlignClipStart(),
                                pLocFrag->nGetAlignClipEnd(),
                                nConsPosLeft_,
                                 nConsPosRight_ ) ) continue;

      aArrayOfReadsToTag_.insert( pLocFrag );
   }


   for( nRead = 0; nRead < aArrayOfReadsToTag_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToTag_[ nRead ];
      aOldTagArrays_.insert( pLocFrag->aTags_ );
   }


   for( nRead = 0; nRead < aArrayOfReadsToTag_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToTag_[ nRead ];

      tag* pTag = new tag( pLocFrag,
                           NULL, // contig?
                           soTagType_,
                           nConsPosLeft_,
                           nConsPosRight_,
                           true, // bWriteToPhdFileNotAceFile_
                           soComment_,
                           "consed",
                           soEmptyString, // current date
                           false );  // bNoTrans

      pLocFrag->addTag( pTag );

      aArrayOfTagsAdded_.insert( pTag );
   }
}



void editAddTagsToAllReadsAtConsPos :: undoEditSpecific() {

   for( int nRead = 0; nRead < aArrayOfReadsToTag_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToTag_[ nRead ];

      pLocFrag->aTags_ = aOldTagArrays_[ nRead ];
   }

   aArrayOfTagsAdded_.clearAndDestroy();
}




void editAddTagsToAllReadsAtConsPos :: writeEditToEditHistoryFile() {


   RWCString soLineToWrite = "addColumnOfReadTags " + soTagType_ + " " +
      pContig_->soGetName() + " " + RWCString( (long) nConsPosLeft_ ) + 
      " " + RWCString( (long) nConsPosRight_ );

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

   if ( !soComment_.bIsNull() ) {
      ConsEd::pGetAssembly()->writeEditToEditHistoryFile(
            "BEGIN_COMMENT" );

      RWCString soTemp = soComment_.stripWhitespace( RWCString::TRAILING );

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

      ConsEd::pGetAssembly()->writeEditToEditHistoryFile(
            "END_COMMENT" );
   }

}



RWCString editAddTagsToAllReadsAtConsPos :: soGetDescriptionOfEdit() {

   RWCString soDescription = "tagAllReads " + soTagType_ + " in " +
      pContig_->soGetName() + " from " + 
      RWCString( (long) pContig_->nUnpaddedIndex( nConsPosLeft_ ) ) +
      " to " +
      RWCString( (long) pContig_->nUnpaddedIndex( nConsPosRight_ ) );

   return( soDescription );
}





void editAddTagsToAllReadsAtConsPos :: setChangedIfNecessary() {

   bOldContigChanged_ = pContig_->bChanged();
   bOldAssemblyChanged_ = ConsEd::pGetAssembly()->bChanged();

   for( int nRead = 0; nRead < aArrayOfReadsToTag_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToTag_[ nRead ];

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



void editAddTagsToAllReadsAtConsPos :: undoSetChangedIfNecessary() {

   for( int nRead = 0; nRead < aArrayOfReadsToTag_.length(); ++nRead ) {
      LocatedFragment* pLocFrag = aArrayOfReadsToTag_[ nRead ];

      if ( !aOldReadsChanged_[ nRead ] ) {
         pLocFrag->setUnchanged();
      }

   }

   if ( !bOldContigChanged_ ) {
      pContig_->setUnchanged();
   }

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