/*****************************************************************************
#   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 phaster2PhdBall_included
#define phaster2PhdBall_included

#include    "rwtvalorderedvector.h"
#include    "filename.h"
#include    "mbtValOrderedVectorOfLong.h"
#include    "mbtValOrderedVectorOfRWCString.h"
#include    <stdio.h>
#include    "mbtPtrOrderedVector.h"
#include    "rwtvalvector.h"



class desiredLocation {
public:
   long lGenomicLocationA_;
   long lGenomicLocationB_;
   RWCString soChromosome_;
   long l1ChrPosA_;
   long l1ChrPosB_; // additional site or end of window
   char cAllowedAllelesA_;
   char cAllowedAllelesB_;
   enum { cMatchOneSite = 'o', cMatchBothSites = 'b', cMatchWindow = 'w' };
   char cTypeOfMatch_;
   bool bMateUnmapped_;
   FileName filPhdBall_;
   FILE* pPhdBall_;

   RWTValVector<int>* paReadDepth_;

public:
   desiredLocation( const bool bMateUnmapped,
                    const RWCString& soChromosome, const long l1ChrPos,
                    const char cTypeOfMatch, 
                    const FileName& filPhdBall ) :
      bMateUnmapped_( bMateUnmapped ),
      soChromosome_( soChromosome ),
      l1ChrPosA_( l1ChrPos ),
      l1ChrPosB_( l1ChrPos ),
      cAllowedAllelesA_( 'n' ),
      cAllowedAllelesB_( 'n' ),
      cTypeOfMatch_( cTypeOfMatch ),
      filPhdBall_( filPhdBall ),
      paReadDepth_(0) {}

   desiredLocation() {}
      
   bool operator==( const desiredLocation& myDesiredSite ) const {
      return( lGenomicLocationA_ == myDesiredSite.lGenomicLocationA_ );
   }

   bool operator<( const desiredLocation& myDesiredSite ) const {
      return ( lGenomicLocationA_ < myDesiredSite.lGenomicLocationA_ );
   }
      
};



#define nMAXLINESIZEB 10000


class phaster2PhdBall {
public:
   phaster2PhdBall( const FileName& filPhasterFOF,
                    const FileName& filPhasterLocations,
                    const FileName& filPhdBallFOF ) :
      filPhasterFOF_( filPhasterFOF ),
      filPhasterLocations_( filPhasterLocations ),
      filPhdBallFOF_( filPhdBallFOF ),
      bConversionTableSet_( false ),
      soLastChromosome_( "not-a-chromosome-name" ),
      nHits_( 0 ),
      soLine_( (size_t) nMAXLINESIZEB ) {}


   void doIt();
   void searchOnePhasterFile( const FileName& filPhasterFile );

   void saveReadPair( const int nIndexOfLocation );

   void writeReadToPhdBall( const int nIndexOfLocation,
                            const RWCString& soReadName,
                            const RWCString& soBases,
                            const RWTValOrderedVector<int>& aQualities,
                            const char cFirstOrSecondRead );

   void convertQualities( 
                         const RWCString& soEncodedQualities,
                         RWTValOrderedVector<int>& aQualities );


   long lConvertToGenomic( const RWCString& soChromosome,
                           const long l1ChrPos );

   void parseLocationsFile();
   void parsePhasterLineCrudely();
   void parsePhasterLineFinely();
   void considerEachSnpForThisReadPair( bool& bSavedReadPair );


   enum { cREAD1 = '1', cREAD2 = '2' };
   enum { cSITEA = 'a', cSITEB = 'b' };

   bool bAlleleOK( desiredLocation* pDL, 
                   const char cWhichRead,
                   const char cWhichSite );

   void setGenomicLocationsOfDesiredLocations();

   void convertFromGenomic( const long lGenomic,
                            RWCString& soChromosome,
                            int& n1ChrPos );

   void openPhdBalls();
   void closePhdBalls();


   void setReadDepthArrays();
   void writeNewLocationsFile();


public:
   FileName filPhasterFOF_;
   FileName filPhasterLocations_;
   FileName filPhdBallFOF_;
   FILE* pPhdBallFOF_;
   FileName filCurrentPhasterFile_;

   // just the lines from the phaster file
   mbtPtrOrderedVector<desiredLocation> aDesiredLocations_;

   FILE* pNewLocations_;

   // for conversion of the desired locations in chromosome and chr pos
   // to phaster genomic coordinates

   bool bConversionTableSet_;
   mbtValOrderedVectorOfRWCString aConvertChromosomes_;
   mbtValOrderedVectorOfLong aConvertStarts_;
   mbtValOrderedVectorOfLong aConvertEnds_;

   // caches for lConvertToGenomic
   RWCString soLastChromosome_;
   int nLastChromosomeIndex_;


   RWCString soDateTimeForTimestamp_;
   RWCString soDateTimeForWRItems_;

   int nHits_;  // a pair is counted as 1


   // current read being parsed

   bool bCurrentPhasterLineIsFinelyParsed_;
   RWCString soReadName_;
   int nRead1Left_;
   int nRead2Left_;
   int nRead1Right_;
   int nRead2Right_;
   long lGenomicLeftRead1_;
   long lGenomicLeftRead2_;
   
   // these are safely further  than
   // the right end of the read in the alignment
   
   long lGenomicFarRightRead1_;
   long lGenomicFarRightRead2_;

   // these are the precise right ends of the reads
   // in alignment to genomic.  I only calculate these
   // if, using the above right ends, the read has a
   // chance of being selected.

   long lGenomicRightRead1_;
   long lGenomicRightRead2_;

   RWCString soEncodedBasesRead1_;
   RWCString soEncodedBasesRead2_;
   RWCString soEncodedQualitiesRead1_;
   RWCString soEncodedQualitiesRead2_;
   bool bTwoReads_;
   long lMaxRight_;

   RWCString soDecodedBasesRead1_;
   RWCString soDecodedBasesRead2_;
   RWCString soDecodedGenomicBasesRead1_;
   RWCString soDecodedGenomicBasesRead2_;

   
   RWCString soLine_;


};


#endif