/*****************************************************************************
#   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 fixContigEnd_included
#define fixContigEnd_included

#include    "rwtptrorderedvector.h"
#include    "filename.h"
#include    "compareContigsTypes.h"
#include    "contigSegment.h"
#include    "rwtvalorderedvector.h"
#include    "assert.h"

class Contig;
class LocatedFragment;
class Assembly;
class paddedPieceOfRead;

class fixContigEnd {
public:
   Contig* pBigContig_;
   int nWhichEnd_;

   Contig* pMiniContig_;

   Assembly* pMiniAssembly_;

   int nLeftmostConsPosOfProtrudingReads_;

   RWTPtrOrderedVector<LocatedFragment> aProtrudingReads_;
   RWTPtrOrderedVector<LocatedFragment> aNewReads_;


   paddedPieceOfRead* pPaddedPieceOfReadBigC_;
   paddedPieceOfRead* pPaddedPieceOfReadMini_;

   // for cleanup
   RWCString soBaseNameForTemporaryFiles_;


   // for joining contigs

   Contig* pNewContig_;

   RWTValOrderedVector<contigSegment> contigSegments_;

   int nInNewJoinedContigAlignedRegionLeftConsPos_;
   int nInNewJoinedContigAlignedRegionRightConsPos_;

public:

   fixContigEnd( Contig* pBigContig, const int nWhichEnd ) :
      pBigContig_( pBigContig ), nWhichEnd_( nWhichEnd ),
      pMiniAssembly_( NULL ) {}

   void doIt( Contig*& pContig );

   void createNewContig();

   void alignMiniContigToBigContig( bool& bError );

   void reportMessage( const bool bError,
                       const RWCString& soError );

   void openAceFileAndChooseContig( 
                        const FileName& filAceFileName,
                        bool& bError );

   int nOpenAceFileAndGetNumberOfContigs( const FileName& filAceFileName );

   void moveMiniAssemblyIntoMainAssembly();

   void addColumnsOfPadsToAlignContigs();

   bool bCheckAddColumnsOfPadsToAlignContigs();
   bool bContigSegmentsOK( );
   void calculateTotalQualitiesOfContigSegment( contigSegment& cs );

   void getBestContigSegment( const int nContigSeg,
                              Contig*& pBestContig,  
                              int& nBestPaddedStart,
                              int& nBestPaddedEnd );

   void addContigSegment( const int nUnpaddedStart1,
                          const int nUnpaddedEnd1,
                          const int nUnpaddedStart2,
                          const int nUnpaddedEnd2 );


   void findEndOfDiscrepantSegment(
                                   const int nPaddedStart,  
                                   // zero-based paddedPieceOfRead coordinates
                               int& nPaddedEnd, 
                                   // zero-based paddedPieceOfRead coordinates
                               int& nUnpaddedEnd1,
                               // in unpadded pContig1_ coordinates
                               int& nUnpaddedEnd2,
                               // in unpadded pContig2_ coordinates
                                   bool& bEndOfAlignment );

   void findEndOfMatchSegment(
                            const int nStartPadded,
                            int& nEndPadded,
                            int& nEndUnpadded1,
                            int& nEndUnpadded2,
                            bool& bMatchSegmentExists );


   paddedPieceOfRead* pGetPaddedPieceOfRead( 
                            const compareContigsTypes eContig1OrContig2 ) {

      if (eContig1OrContig2 == eContig1 )
         return( pPaddedPieceOfReadBigC_ );
      else if ( eContig1OrContig2 == eContig2 )
         return( pPaddedPieceOfReadMini_ );
      else
         assert( false );
   }


   void makeContigSegmentsContiguous( 
            Contig* pLeftContig,
            const int nNewConsPosFromNotLeftConsPos );

   void dumpContigSegments();

   void cleanUp();

   void getLeftAndRightEndsOfFakeRead( 
         int& nPaddedLeftEndOfFakeRead, 
         int& nPaddedRightEndOfFakeRead );


};

#endif