/*****************************************************************************
#   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 basesAndQualitiesAndPeaks_included
#define basesAndQualitiesAndPeaks_included

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



class basesAndQualitiesAndPeaks {
public:
   RWCString soBases_;
   RWTValOrderedVector<unsigned char> aQualities_;

   RWTValOrderedVector<int>* pBigPeakPositions_;
   RWTValOrderedVector<short int>* pLittlePeakPositions_;

   enum { cNone = 'n', cBig = 'b', cLittle = 'l' };

   char cWhichPeakPositionsAreUsed_; // 'n' none, 'b' big, 'l' little
   

   RWCString soSequenceName_;

   // these correspond to clip_left and clip_right in sffinfo.c or
   // readOneSffFile.cpp  Note that they apparently are 1-based, unlike
   // most of the other positions in these files that are 0-based.

   int n1ClipLeft_;
   int n1ClipRight_;


   int nTraceArrayMaxIndex_; 
   // typically, this is numBases*19 + 12
   // However, for paired reads or trimmed reads, it may be something else 
   // since the trace may be much larger than the read


public:

   void createPointPosArray( const bool bFoundTraceArrayMaxIndex, 
                             const int nTraceArrayMaxIndex,
                             const size_t nInitialSizeOfArray,
                             const bool bFillUpArray );


   void createPointPosArray2( const char cWhichPeakPositionsAreUsed,
                              const size_t nInitialSizeOfArray,
                              const bool bFillUpArray );

   int nGetPointPos(const int n0PaddedSeqPos ) const;

   void appendPointPos( const int nPointPos );


   bool bHasPeakPositions() {
      return( cWhichPeakPositionsAreUsed_ != cNone );
   }


   void setPointPosArraySubstring( 
               const basesAndQualitiesAndPeaks* pBigRead,
               const int n0Start,
               const int nLength );

   void reverseComplementThyself();


};


#endif