/*****************************************************************************
#   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 phdBall2Fasta_included
#define phdBall2Fasta_included

#include    <cstdio>
using namespace std;
#include    "filename.h"
#include    "rwtvalorderedvector.h"

const int nMaxLineSize2 = 10000;

class phdBall2Fasta {
public:
   phdBall2Fasta( const FileName& filPhdBall, const FileName& filFasta,
                  const FileName& filFastq ) :
      filPhdBall_( filPhdBall ), filFasta_( filFasta ), 
      filFastq_( filFastq ) {}

   void doIt();

   void readFileOfPhdFilesForPhdBall2Fasta(
            FILE* pPhdBall,
            RWCString& soFastaHeader,
            RWCString& soFastaQualHeader,
            RWCString& soBases,
            RWTValOrderedVector<int>& aQualities,
            bool& bEndOfFile );

   void readFirstBeginSequenceLine( FILE* pPhdBall,
                                    bool& bEndOfFile );

   void readWholeReadItemForPhdBall2Fasta( FILE* pFil, 
                                           RWCString& soFastaHeader );

   void parsePrimerWRItemForPhdBall2Fasta( const int nDataLine, 
                                           RWCString& soFastaHeader );

   void parseTemplateWRItemForPhdBall2Fasta( const int nDataLines, 
                                             RWCString& soFastaHeader );

   float fGetMeanQuality( const RWTValOrderedVector<int>& 
                          aQualities );

public:
   FileName filPhdBall_;
   FileName filFasta_;
   FileName filQualities_;
   FileName filFastq_;
   
   int nLine_;
   char szLine_[ nMaxLineSize2 ];

};

#endif