/*****************************************************************************
#   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    "contigMatchTablesType.h"
#include    "nConvertFrom4Mer.h"
#include    <cstdlib>
using namespace std;
#include    "assert.h"
#include    "nLengthOf4Mer.h"


void setMatchLookupTable( contigMatchTablesType* pUnpaddedContig ) {

   // initialize the first blocks

   for( int n4Mer = 0; n4Mer < nNumberOf4Mers; ++n4Mer ) {
      pUnpaddedContig->blockOfLocationsOfA4Mer_[ n4Mer].nCurrentLength_ = 0;
      pUnpaddedContig->blockOfLocationsOfA4Mer_[ n4Mer].pNextBlockOfLocationsOfA4Mer_ = 0;
      pUnpaddedContig->pArrayOfLastBlocks_[ n4Mer ] =
         pUnpaddedContig->blockOfLocationsOfA4Mer_ + n4Mer;
   }

   for( int nZeroBasedUnpadded = 0; 
        nZeroBasedUnpadded < pUnpaddedContig->nUnpaddedBases_ - nLengthOf4Mer + 1;
        ++nZeroBasedUnpadded ) {

      int n4Mer = nConvertFrom4Mer( 
               &( pUnpaddedContig->szUnpaddedBases_[ nZeroBasedUnpadded ] )
               );

      blockOfLocationsOfA4MerType* pBlockOfLocationsOfA4Mer = 
         pUnpaddedContig->pArrayOfLastBlocks_[ n4Mer ];

      // if the last blockOfLocationsOfA4Mer is full, allocate
      // another one

      if ( pBlockOfLocationsOfA4Mer->nCurrentLength_ >= n10 ) {
         pBlockOfLocationsOfA4Mer->pNextBlockOfLocationsOfA4Mer_ =
            (blockOfLocationsOfA4MerType*) malloc( 
                       sizeof( blockOfLocationsOfA4MerType )
                                                   );
         pBlockOfLocationsOfA4Mer = 
            pBlockOfLocationsOfA4Mer->pNextBlockOfLocationsOfA4Mer_;

         assert( pBlockOfLocationsOfA4Mer );
         pBlockOfLocationsOfA4Mer->nCurrentLength_ = 0;
         pBlockOfLocationsOfA4Mer->pNextBlockOfLocationsOfA4Mer_ = 0;
         pUnpaddedContig->pArrayOfLastBlocks_[ n4Mer ] =
            pBlockOfLocationsOfA4Mer;
      }

      int nCurrentSubscript = pBlockOfLocationsOfA4Mer->nCurrentLength_;
      pBlockOfLocationsOfA4Mer->nUnpaddedPosition_[ nCurrentSubscript ] =
         nZeroBasedUnpadded + 1;
      ++pBlockOfLocationsOfA4Mer->nCurrentLength_;

   }

}