/*****************************************************************************
#   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 digestForOneEnzyme_included
#define digestForOneEnzyme_included

#include    "rwtptrorderedvector.h"
#include    "arrayOfRestrictionFragments.h"

class restrictionFragment;
class guiDisplayDigest;

class digestForOneEnzyme {
public:
   // these are for building the aPredictedResFragsBySize_
   arrayOfRestrictionFragments
       aPredictedRestrictionFragmentsNotEndingAtVectorInsertJunction_;
   arrayOfRestrictionFragments
       aPredictedInsertRestrictionFragmentsEndingAtVectorInsertJunction_;
   arrayOfRestrictionFragments
       aPredictedVectorRestrictionFragmentsEndingAtVectorInsertJunction_;

   bool bNoCutSitesInVector_;

   arrayOfRestrictionFragments aActualRestrictionFragments_;
   arrayOfRestrictionFragments aPredictedResFragsBySize_;
   // this is the same array as above, but sorted by position in scaffold
   arrayOfRestrictionFragments aPredictedResFragsByConsPos_;


   RWCString soEnzymeName_;
   RWCString soEnzymeBases_;

   int nMaxGelPosition_;

   guiDisplayDigest* pGuiDisplayDigest_;
   int nAssemblyViewEnzymeLine_;


public:
   digestForOneEnzyme() : bNoCutSitesInVector_( false ),
                          nAssemblyViewEnzymeLine_( -1 ) {
      aPredictedRestrictionFragmentsNotEndingAtVectorInsertJunction_.soName_ =
         "digestForOneEnzyme::aPredictedRestrictionFragmentsNotEndingAtVectorInsertJunction_";
      aPredictedInsertRestrictionFragmentsEndingAtVectorInsertJunction_.soName_ =
         "digestForOneEnzyme::aPredictedInsertRestrictionFragmentsEndingAtVectorInsertJunction_";
      aPredictedVectorRestrictionFragmentsEndingAtVectorInsertJunction_.soName_
         = 
         "digestForOneEnzyme::aPredictedVectorRestrictionFragmentsEndingAtVectorInsertJunction_";
      aActualRestrictionFragments_.soName_ =
         "digestForOneEnzyme::aActualRestrictionFragments_";
      
      aPredictedResFragsBySize_.soName_ =
         "digestForOneEnzyme::aPredictedResFragsBySize_";

      aPredictedResFragsByConsPos_.soName_ =
         "digestForOneEnzyme::aPredictedResFragsByConsPos_";
   }

   ~digestForOneEnzyme();
   bool operator==( const digestForOneEnzyme& dig2 ) const {
      return( this == &dig2 );
   }


   void processingAfterFindingAllPartialFragments(  
           const bool bFlipVectorFromTheDefault);

   void combineFragments( 
          restrictionFragment* pInsertFrag,
          const int nWhichEndOfInsert,
          const int nWhichEndOfVector,
          restrictionFragment*& pNewFrag );

   void combineFragments2(
      restrictionFragment* pPartialInsertFragment,
      restrictionFragment* pPartialVectorFragment,
      restrictionFragment*& pNewFrag );

   void combineRemainingVectorAndInsertPartialFragments( 
            const bool bFlipVectorFromDefault );

   restrictionFragment* pGetClosestAvailableFragment(
         restrictionFragment* pFrag,
         RWTPtrOrderedVector<restrictionFragment>* pFragmentArray );

   restrictionFragment* pGetClosestAvailableFragment2( 
         restrictionFragment* pFrag,
         RWTPtrOrderedVector<restrictionFragment>* pFragmentArray );


   void relatePredictedAndActualFragments();


   bool bRelateMorePredictedAndActualFragments();

   void dealWithPartialFragments( const bool bFlipVectorFromDefault );

};


#endif