/*****************************************************************************
#   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    "rwcstring.h"
#include    "tagsGotoList.h"
#include    "contig.h"
#include    "locatedFragment.h"
#include    "tag.h"



static char* szGotoItemDesc = "tags";

static const int nMaxLengthForDescription = 51;


tagsGotoList :: tagsGotoList(Contig* pContig, const RWCString& soTagTypeOfList )
{

   // first add read tags

   int nNumFrags = pContig->nGetNumberOfFragsInContig();
   for (int nFrag = 0; nFrag < nNumFrags; nFrag++) {

      // get pointer to this located frag from contig
      LocatedFragment* pLocFrag = pContig->pLocatedFragmentGet(nFrag);
      
      for( int nTag = 0; nTag < pLocFrag->nGetNumberOfTags(); ++nTag ) {
         tag* pTag = pLocFrag->pGetTag( nTag );
         
         if (pTag->soGetTagType() == soTagTypeOfList ) {

            int nConsPosStart = pTag->nPaddedConsPosStart_;
            int nConsPosEnd = pTag->nPaddedConsPosEnd_;

            int nUnpaddedConsPosStart = 
               pContig->nUnpaddedIndex( nConsPosStart );

            int nUnpaddedConsPosEnd =
               pContig->nUnpaddedIndex( nConsPosEnd );

            RWCString soDescription = 
               pTag->soGetExtraInformationForNavigator( nMaxLengthForDescription );

            if ( soDescription.isNull() ) {
               char szTemp[500];
               sprintf( szTemp, "%6d %s", 
                        ( nUnpaddedConsPosEnd - nUnpaddedConsPosStart + 1 ),
                        (char*) soTagTypeOfList.data() );
               soDescription = szTemp;
            }


            gotoItem* pGotoItem = new gotoItem( pContig,
                                                pLocFrag,
                                                nConsPosStart,
                                                nConsPosEnd,
                                                nUnpaddedConsPosStart,
                                                nUnpaddedConsPosEnd,
                                                soDescription
                                                );

            addToList( pGotoItem );
         } // if (pTag->soGetTagType...
      } // for( int nTag ...
   } // for (int nFrag = 0 ...


   // now add consensus tags

   for( int nConsensusTag = 0; nConsensusTag < pContig->nGetNumberOfTags();
        ++nConsensusTag ) {
      
      tag* pTag = pContig->pGetTag( nConsensusTag );

      if (pTag->soGetTagType() == soTagTypeOfList ) {

         int nConsPosStart = pTag->nPaddedConsPosStart_;
         int nConsPosEnd = pTag->nPaddedConsPosEnd_;

         int nUnpaddedConsPosStart = 
            pContig->nUnpaddedIndex( nConsPosStart );

         int nUnpaddedConsPosEnd =
               pContig->nUnpaddedIndex( nConsPosEnd );

         RWCString soDescription = 
            pTag->soGetExtraInformationForNavigator( nMaxLengthForDescription );

         if ( soDescription.isNull() )
            soDescription = soTagTypeOfList;

         gotoItem* pGotoItem = new gotoItem( pContig,
                                             NULL, // LocatedFragment
                                             nConsPosStart,
                                             nConsPosEnd,
                                             nUnpaddedConsPosStart,
                                             nUnpaddedConsPosEnd,
                                             soDescription
                                             );

         addToList( pGotoItem );
      } // if (pTag->soGetTagType...
   }

   sortByPosition();
}