/*****************************************************************************
#   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 PADDEDPIECEOFREAD_INCLUDED
#define PADDEDPIECEOFREAD_INCLUDED

#include    "rwcstring.h"
#include    "rwtvalorderedvector.h"
#include    "quality.h"

class Contig;

class paddedPieceOfRead {
public:
  RWCString soName_;
  RWCString soBasesAndPads_;
  int nUnpaddedOffset_;
   // This is not the unpadded position of the first base in the alignment.
   // In fact, the first base could be a pad.  (or could it?)  Instead,
   // this is the unpadded position of the first non-pad before the
   // alignment.  Thus you add this to the number of non-pads to get
   // the unpadded position of a base in the alignment
  Contig* pContig_;

   // unpadded positions within the contig of the aligned region
  int nUnpaddedAlignmentStart_;
  int nUnpaddedAlignmentEnd_;

   // these are *not* the padded equivalent of
   // nUnpaddedAlignmentStart_ and nUnpaddedAlignmentEnd_.  There are
   // unaligned context bases at the beginning and end of
   // soBasesAndPads_.  These numbers give the 0-based positions
   // within soBasesAndPads_ which are aligned.

  int nPaddedAlignmentStart_;
  int nPaddedAlignmentEnd_;

  bool bComplemented_;
   // soBasesAndPads_ is complemented from the way pContig is
   // all of the other nUnpaddedAlignmentStart_ and nPaddedAlignmentStart_
   // are with respect to pContig positions.

  // preserve a copy of the base qualities so that people can modify
  // the actual consensus while they are looking at the alignment
  RWTValOrderedVector<Quality> aBaseAndPadQualities_;

public:
  int nGetPaddedLength() { return( soBasesAndPads_.length() ); }

  int nUnpaddedContigPosFromZeroBasedPaddedPos( const int nZeroBasedPaddedPos );
   
  int nZeroBasedAlignPosFromUnpadded( const int nSourceUnpadded );
  int nGetRightMostUnpaddedConsPosOfAlignment();
  int nGetLeftMostUnpaddedConsPosOfAlignment();
  
  paddedPieceOfRead( const RWCString& soNameForDebugging,
                     const RWCString& soBasesAndPads,
                     const int nZeroBasedPaddedPosOfKnownBase, // wrt soBasesAndPads
                     const int nConsPosOfKnownBase, // wrt pContig
                     Contig* pContig,
                     const int nUnpaddedAlignmentStart, // wrt pContig
                     const int nUnpaddedAlignmentEnd, // wrt pContig
                     const int nPaddedAlignmentStart, // wrt soBasesAndPads
                     const int nPaddedAlignmentEnd, // wrt soBasesAndPads
                     const bool bComplemented );

  void calculateQualities();
};

#endif