/*****************************************************************************
#   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    <cstdlib>
using namespace std;
#include    "paddedFromUnpadded.h"
#include    "contig.h"
#include    "assert.h"


int paddedFromUnpadded :: nPaddedFromUnpadded( const int nUnpaddedConsPos ) {

   if ( nUnpaddedConsPos < nMinUnpaddedConsPos_ ) {
      int nAmountBeforeConsensus = nMinUnpaddedConsPos_ - nUnpaddedConsPos;
      int nPaddedConsPos = pContig_->nGetStartConsensusIndex() -
         nAmountBeforeConsensus;

      return( nPaddedConsPos );
   }
   else if ( nUnpaddedConsPos > nMaxUnpaddedConsPos_ ) {
      int nAmountAfterConsensus = nUnpaddedConsPos - nMaxUnpaddedConsPos_;
      int nPaddedConsPos = pContig_->nGetEndConsensusIndex() +
         nAmountAfterConsensus;

      return( nPaddedConsPos );
   }
   else {
      return( pPaddedConsensusPositions_[ nUnpaddedConsPos - nMinUnpaddedConsPos_ ] );
   }
}



void paddedFromUnpadded :: setPaddedPositionsArray() {

   int nCurrentSizeOfArray = nMaxUnpaddedConsPos_ - nMinUnpaddedConsPos_ + 1;

   nMinUnpaddedConsPos_ = pContig_->nGetUnpaddedStartIndex();
   // don't trust any stored information from unpaddedFromPadded
   // see C++ FAQS 101 for syntax
   int nUnpaddedLength = pContig_->Sequence::nGetUnpaddedSeqLength();

   nMaxUnpaddedConsPos_ = nMinUnpaddedConsPos_ + nUnpaddedLength - 1;

   if ( pPaddedConsensusPositions_  ) {

      if ( nCurrentSizeOfArray < nUnpaddedLength )
         allocateMemory( nUnpaddedLength );
      // otherwise, no need to allocate memory
   }
   else
      allocateMemory( nUnpaddedLength );


   Ntide nt;
   int nUnpaddedConsPos = nMinUnpaddedConsPos_;
   for( int nPadded = pContig_->nGetStartConsensusIndex();
        nPadded <= pContig_->nGetEndConsensusIndex();
        ++nPadded ) {
      
      nt = pContig_->ntGetConsUnsafeOnConsensus( nPadded );
      if (! nt.bIsPad() ) {
         pPaddedConsensusPositions_[ nUnpaddedConsPos - nMinUnpaddedConsPos_ ]
            = nPadded;
         ++nUnpaddedConsPos;
      }
   }

   assert( ( nUnpaddedConsPos - 1 ) == nMaxUnpaddedConsPos_ );
}


void paddedFromUnpadded :: allocateMemory( const int nUnpaddedLength ) {

   pPaddedConsensusPositions_ = (int*) malloc( 
                                  sizeof( int ) * nUnpaddedLength );

   assert( pPaddedConsensusPositions_ );

}

   
paddedFromUnpadded :: paddedFromUnpadded( Contig* pContig ) :
   pContig_( pContig ),
   nMinUnpaddedConsPos_( 0 ),
   nMaxUnpaddedConsPos_( 0 ),
   pPaddedConsensusPositions_( NULL )
{}