/*****************************************************************************
#   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 seqMatch_included
#define seqMatch_included


#include    <Xm/Xm.h>
#include    "bool.h"


class Contig;



class seqMatch {
public:
   seqMatch( Contig* pContig1,
             Contig* pContig2,
             const int nStart1,
             const int nStart2,
             const int nEnd1,
             const int nEnd2,
             const bool bComplemented,
             const float fPercentSimilar );


   // default copy ctor already does this, and does it more reliably 
   // with additional member data
//    seqMatch( const seqMatch* pSeqMatch ) {
//       pContig_[0] = pSeqMatch->pContig_[0];
//       pContig_[1] = pSeqMatch->pContig_[1];
//       nUnpaddedStartConsPos_[0] = pSeqMatch->nUnpaddedStartConsPos_[0];
//       nUnpaddedStartConsPos_[1] = pSeqMatch->nUnpaddedStartConsPos_[1];
//       nUnpaddedEndConsPos_[0] = pSeqMatch->nUnpaddedEndConsPos_[0];
//       nUnpaddedEndConsPos_[1] = pSeqMatch->nUnpaddedEndConsPos_[1];
//       bComplemented_ = pSeqMatch->bComplemented_;
//       nScaffold_[0] = pSeqMatch->nScaffold_[0];
//       nScaffold_[1] = pSeqMatch->nScaffold_[1];
//       nScaffoldPosStart_[0] = pSeq


//    }

   bool operator==( const seqMatch& seqq ) const {
      return( this == &seqq );
   }

   GC gcGet();

   inline int nGetBezierX( const int nArc, const float fT ) {
      int n = 
         0.5 + // for rounding
         fAX_[ nArc ] * fT*fT*fT +
         fBX_[ nArc ] * fT*fT +
         fCX_[ nArc ] * fT +
         fDX_[ nArc ];
      return n;
   }

   inline int nGetBezierY( const int nArc, const float fT ) {
      int n =
         0.5 + // for rounding
         fAY_[ nArc ] * fT*fT*fT +
         fBY_[ nArc ] * fT*fT +
         fCY_[ nArc ] * fT +
         fDY_[ nArc ];
      return n;
   }

   bool bOKToShow();
         

public:
   // indexed by the copy of the repeat
   Contig* pContig_[2];
   int nUnpaddedStartConsPos_[2];
   int nUnpaddedEndConsPos_[2];
   // perhaps we should also have which scaffold and scaffold positions
   // my understanding (Dec 2002):
   // nUnpaddedStartConsPos_[0] goes to nUnpaddedStartConsPos_[1]
   // and 
   // nUnpaddedEndConsPos_[0] goes to nUnpaddedEndConsPos_[1]
   // nUnpaddedStartConsPos_[0] <= nUnpaddedEndConsPos_[0]
   // but no guarantees about
   // nUnpaddedStartConsPos_[1] <=> nUnpaddedEndConsPos_[1]

   bool bComplemented_;

   // indexed by the copy of the repeat
   // The arc goes from start to start
   // and from end to end, regardless
   // whether complemented or not.  These are not necessarily set--
   // could not be set if the seqMatch is not visible.
   int nScaffold_[2];
   int nScaffoldPosStart_[2];
   int nScaffoldPosEnd_[2];

   bool bDirectNotInverted_;
   
   float fPercentSimilar_; // some measure of the similarity of the
   //   sequences.--perhaps % similar since that is what many people will
   //   understand

   // there are 2 arcs for a matching region, so two sets
   // of Bezier coefficients.  These are indexed by the arcs--not
   // the regions
   float fAX_[2];
   float fBX_[2];
   float fCX_[2];
   float fDX_[2];
                
   float fAY_[2];
   float fBY_[2];
   float fCY_[2];
   float fDY_[2];

   int nNumberOfPointsForDrawing_[2];
   
   bool bInView_[2]; // this would be false if the contig wasn't
   // displayed in assemblyView, or if the curve was off the visible screen.


};


#endif