/*****************************************************************************
#   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 regionToAmplify_included
#define regionToAmplify_included


#include    "rwtvalorderedvector.h"
#include    "rwtptrorderedvector.h"
#include    "regionOfContig.h"
#include    "pcrPrimer.h"
#include    "regionOfContig.h"
#include    "pcrPrimerrPair.h"
#include    "pcrPrimerPairSubscripts.h"


class regionToAmplify {
public:
   RWCString soRegionID_;
   regionOfContig region1_;
   bool bPrimersInRegion1PointRightNotLeft_;
   regionOfContig region2_;
   bool bPrimersInRegion2PointRightNotLeft_;
   bool bBiggestNotSmallest_;
   

   RWTPtrOrderedVector<pcrPrimer> aPCRPrimersRegion1_;
   RWTPtrOrderedVector<pcrPrimer> aPCRPrimersRegion2_;
   int nProductSizeOfBestPair_;


   // stuff used in findPCRPrimerPairToCloseGap for autoFinishPCR:

   int nLastUsedIndexA_;
   int nLastUsedIndexB_;
   bool bFoundAPair_;
   int nMaxProductSize_;
   int nBestAIndex_; 
   int nBestBIndex_; 
   int nSmallestProductSize_;
   RWTValOrderedVector<pcrPrimerPairSubscripts> aAcceptablePCRPrimerPairs_;

public:
   void findPCRPrimerPair();
   void checkRegionForAcceptablePrimersWithNotTooManyFalseMatches( 
                           const regionOfContig& region,
                           const bool bPrimersPointRightNotLeft,
                           const bool bRegion1NotRegion2 );

   void makeOnePrimerOutOfRegion( 
                           const regionOfContig& region,
                           const bool bPrimersPointRightNotLeft,
                           const bool bRegion1NotRegion2 );

   regionToAmplify();
   ~regionToAmplify();

   bool bIsThereAnAcceptablePrimerWithThis3PrimeEnd(
        primerType* pSamplePrimer,
        primerType*& pShortestAcceptablePrimer,
	int& nWhyIsPrimerNotAcceptable );

   void sortPCRPrimerPairs( pcrPrimerrPair*& pBestPCRPrimerPair );

   bool operator==( const regionToAmplify& region ) const {
      return( this == &region );
   }

   void autoFinishPCRToCloseAGap( Contig* pContig1,
                                  const int nWhichEnd1,
                                  Contig* pContig2,
                                  const int nWhichEnd2 );

   void findPCRPrimerPairToCloseGap();


   void findBestAcceptablePCRPrimerPair( pcrPrimerrPair*& pBestPrimerPair );

   void setRegion( const int nWhichRegion,
                   Contig* pContig,
                   const int nWhichEnd,
                   bool& bProblems );

   void calculateDistancesToGap();

   void calculateDistanceToGap( 
         RWTPtrOrderedVector<pcrPrimer>& aPrimer,
         Contig* pContig,
         const bool bRightEndNotLeftEnd );

   void checkSorted( const RWTPtrOrderedVector<pcrPrimer>& aPrimer );

   int nGetIndexFromProductSize( const int nProductSize,
                                 const bool bANotB );

   void processPrimerPair( const int nA,
                           const int nB );

   void replaceBestPrimerPairIfNecessary(
                                         const int nA,
                                         const int nB,
                                         const int nProductSize );

};



#endif