/*****************************************************************************
#   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 restrictionFragment_included
#define restrictionFragment_included

#include    "rwcstring.h"


class Contig;
class GuiColorText;
class digestForOneEnzyme;

class restrictionFragment {
public:

   // the following are used for both actual fragments and predicted
   // fragments
   int nSize_;
   float fPositionOnGel_;

   restrictionFragment* pCorrespondingFrag_;
   enum { ACTUAL_FRAGMENT = 0x1, PREDICTED_FRAGMENT = 0x2 };
   unsigned char cActualOrPredictedFragment_;
   bool bCombinedVectorAndInsertPartialFragments_;

   // the following are used only for predicted fragments

   // a site can either be found in a contig, found in the vector,
   // or not found at all 
   enum fragmentEndType { IN_CONTIG = 0x1, IN_VECTOR = 0x2, UNKNOWN = 0x4,
                          AT_VECTOR_INSERT_JUNCTION = 0x8 };
   fragmentEndType fragLeft_;
   fragmentEndType fragRight_;
   Contig* pLeftContig_;
   Contig* pRightContig_;
   int nUnpaddedLeft_;  //might be position in vector
   int nUnpaddedRight_;
   bool bVectorFragment_;
   int nExtendsOffWhichEndOfContig_;  // only used if the fragment is
   // a composite of an insert fragment and a vector fragment

   int nPositionOrder_; // if sorted by position, sort by this
   bool bPartialFragmentHasBeenPutTogether_;
   bool bIncludesAllOfVector_;
   digestForOneEnzyme* pDigestForOneEnzyme_; 
   // above field
   // currently (2004) only filled in in the case of the
   // restrictionFragments that are part of
   // digestForOneEnzyme::aPrdictedResFragsBySize_ and
   // digestforOneEnzyme::aPredictedResFragsByConsPos_


public:
   restrictionFragment( unsigned char cActualOrPredictedFragment ) 
      : cActualOrPredictedFragment_( cActualOrPredictedFragment ),
      nSize_( 0 ),
      pLeftContig_( 0 ),
      pRightContig_( 0 ),
      pCorrespondingFrag_( 0 ),
      bCombinedVectorAndInsertPartialFragments_( false ),
      bPartialFragmentHasBeenPutTogether_( false ),
      bVectorFragment_( false ),
      bIncludesAllOfVector_( false ),
      pDigestForOneEnzyme_( 0 ) {}

   GuiColorText* pGetGuiColorText();
   void getDescriptionLine( RWCString& soDescription );
   bool operator==( const restrictionFragment& res2 ) const {
      return( this == &res2 );
   }

   RWCString soGetProblemDescription();

   bool bIsProblemFragment();

   bool bIsVectorFragment() {
      if ( fragLeft_ == IN_VECTOR && fragRight_ == IN_VECTOR )
         return( true );
      else
         return( false );
   }

   bool bIsFragmentPartOfThisContig( Contig* pContig );
};

   
#endif