/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef paddedPieceOfSequence_included
#define paddedPieceOfSequence_included


#include    "rwcstring.h"
#include    "bool.h"

class Sequence;

class paddedPieceOfSequence {
public:
   RWCString soBasesAndPads_;
   int nUnpaddedStart_;
   int nUnpaddedEnd_;
   bool bSequenceIsComplemented_;
   // This is the unpadded position of the first non-pad before the alignment
   // Add this to the unpadded position within the alignment to get the
   // unpadded position within the sequence

   Sequence* pSequence_;  // could be either a LocatedFragment or a Contig

public:
   paddedPieceOfSequence( Sequence* pSequence,
                          const int nUnpaddedStart,
                          const int nUnpaddedEnd,
                          const bool bComplemented ) :
      pSequence_( pSequence ),
      nUnpaddedStart_( nUnpaddedStart ),
      nUnpaddedEnd_( nUnpaddedEnd ),
      bSequenceIsComplemented_( bComplemented) {}
   
   bool operator==( const paddedPieceOfSequence ppos ) const {
      return( this == &ppos );
   }

   int nUnpaddedContigPosFromZeroBasedPaddedPos( const int nZeroBasedPaddedPos );

};

#endif