/*****************************************************************************
#   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 countsOfWhyprimersAreNotAcceptable_included
#define countsOfWhyprimersAreNotAcceptable_included


#include    "primerType.h"
#include    "rwcstring.h"

#define ZERO_ALL_COUNTS \
      nTotalPrimersTried_ = 0; \
      nAcceptablePrimers_ = 0; \
      nUnacceptablePrimers_ = 0; \
      nBAD_PRIMER_STICKS_TO_SEQUENCE_IN_FILE_ = 0; \
      nBAD_PRIMER_STICKS_TO_SOMEWHERE_ELSE_ = 0; \
      nBAD_PRIMER_STICKS_TO_SELF_ = 0; \
      nBAD_PRIMER_MELTING_TEMPERATURE_TOO_LOW_ = 0; \
      nBAD_PRIMER_MELTING_TEMPERATURE_TOO_HIGH_ = 0; \
      nBAD_PRIMER_TOO_LOW_QUALITY_ = 0; \
      nBAD_PRIMER_MONONUCLEOTIDE_REPEAT_ = 0; \
      nBAD_PRIMER_HAS_NO_TEMPLATE_ = 0; \
      nBAD_PRIMER_IN_SINGLE_SUBCLONE_REGION_ = 0; \
      nBAD_PRIMER_WHERE_HIGH_QUALITY_DISCREPANCIES_ = 0; \
      nBAD_PRIMER_WHERE_UNALIGNED_HIGH_QUALITY_REGION_ = 0; \
      nBAD_PRIMER_NOT_ENOUGH_TEMPLATES_ = 0; \
      nBAD_PRIMER_NOT_JUST_ACGT_ = 0; \
      nBAD_PRIMER_PAIR_FORMS_PRODUCT_SOMEWHERE_ELSE_ = 0; \
      nBAD_PRIMER_PAIR_FORMS_PRODUCT_WITHIN_OR_ENCLOSING_DESIRED_PRODUCT_ = 0; \
      nBAD_PRIMER_PAIR_TEMP_DIFF_TOO_GREAT_ = 0; \
      nBAD_PRIMER_PAIR_FORMS_PRIMER_DIMER_ = 0;



class countsOfWhyPrimersAreNotAcceptable {
public:
   int nTotalPrimersTried_;
   int nAcceptablePrimers_;
   int nUnacceptablePrimers_;
   int nBAD_PRIMER_STICKS_TO_SEQUENCE_IN_FILE_;
   int nBAD_PRIMER_STICKS_TO_SOMEWHERE_ELSE_;
   int nBAD_PRIMER_STICKS_TO_SELF_;
   int nBAD_PRIMER_MELTING_TEMPERATURE_TOO_LOW_;
   int nBAD_PRIMER_MELTING_TEMPERATURE_TOO_HIGH_;
   int nBAD_PRIMER_TOO_LOW_QUALITY_;
   int nBAD_PRIMER_MONONUCLEOTIDE_REPEAT_;
   int nBAD_PRIMER_HAS_NO_TEMPLATE_;
   int nBAD_PRIMER_IN_SINGLE_SUBCLONE_REGION_;
   int nBAD_PRIMER_WHERE_HIGH_QUALITY_DISCREPANCIES_;
   int nBAD_PRIMER_WHERE_UNALIGNED_HIGH_QUALITY_REGION_;
   int nBAD_PRIMER_NOT_ENOUGH_TEMPLATES_;
   int nBAD_PRIMER_NOT_JUST_ACGT_;
   int nBAD_PRIMER_PAIR_FORMS_PRODUCT_SOMEWHERE_ELSE_;
   int nBAD_PRIMER_PAIR_FORMS_PRODUCT_WITHIN_OR_ENCLOSING_DESIRED_PRODUCT_;
   int nBAD_PRIMER_PAIR_TEMP_DIFF_TOO_GREAT_;
   int nBAD_PRIMER_PAIR_FORMS_PRIMER_DIMER_;
public:
   countsOfWhyPrimersAreNotAcceptable() {
      ZERO_ALL_COUNTS;
   }

   void accountForOnePrimer( const primerType* pPrimer );

   void accountForAllPrimers( primerType* pPrimerArray,
                         const int nNumberOfPrimers );

   void getCountsInString( RWCString& soExplanation );




};




#endif