/*****************************************************************************
#   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 PRIMER_INCLUDED
#define PRIMER_INCLUDED

#include    "bool.h"
#include    "contigMatchTablesType.h"

class Contig;
class subcloneTTemplate;

#define nNUMBER_OF_TEMPLATES 5


typedef struct {
   char* szPrimer_;  // NOT null-terminated!
   // pointer to location in szUnpaddedBases_ in unpaddedContigType
   // In the case of reverse primers, this is the bases from right to
   // left and complemented.  It is the bases of the primer you would
   // actually use in the lab.

   unsigned char* pUnpaddedQualityArray_; // pointer to location
   // in pUnpaddedQualityArray_ in unpaddedContigType

   contigMatchTablesType* pCurrentUnpaddedContig_; 
   // for checking that the memory is still valid.  Otherwise
   // szPrimer_ and pUnpaddedQualityArray_ might point to memory that
   // is either deallocated or else is reused for something else

   Contig* pContig_;
   int  nUnpaddedStart_;
   // warning--in the case of reverse primers, this is still the position
   // of the left-most base in the contig.  The coordinates are not 
   // complemented.  It is as though it were a forward primer.  This is
   // so that the user can find the primer.
   int  nUnpaddedLength_;
   int  nUnpaddedEnd_;
   // see warning for nUnpaddedStart_

   bool bTopStrandNotBottomStrand_;

   double  dMeltingTemperature_;
   unsigned char ucMinQuality_;
   unsigned char ucMinQualityIn3Prime4Bases_; 
   int  n3Prime4Bases_;

   int  nScoreOfStickiestFalseMatch_;
   Contig* pContigOfStickiestFalseMatch_;
   int  nUnpaddedOfStickiestFalseMatch_;
   // This is the position of the left end of the bases that
   // are attempted to be aligned with the primer.  Since only the
   // short primers are checked for false matches, the end of the
   // this corresponding region will be at nUnpaddedOfStickiestFalseMatch_
   // + consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimer_ - 1
   // In the case in which the target contig is complemented, this 
   // unpadded position is in complemented coordinates.

   // If the primer is unacceptable ( bAcceptable_ = false ), then
   // there may be an even worse (stickier) false match.  This particular
   // one was bad enough to exclude the primer, so no attempt was made
   // to find one even worse.  If the primer is acceptable, then this
   // is guaranteed to be the worse false match.

   bool bContigOfStickiestFalseMatchIsComplemented_;

   int  nSelfMatchScore_;
   int  nSelfMatchOffsetOfComplementedPrimer_;
   int  nSelfMatchPosOf3PrimeSubOligo_;

   int  nSequenceInFileStickiestScore_;
   int  nSequenceInFileSequenceNumber_;
   int  nSequenceInFileBasePosition_;
   bool bSequenceInFileIsComplemented_;

   int  nLengthOfMononucleotideRun_;
        // This is not always calculated.  It is calculated
        // only if the other checks pass.
   bool bAcceptable_;
   int  nWhyIsPrimerNotAcceptable_;
   int  nDistanceFromCursor_;
   subcloneTTemplate* pSubcloneTemplate_[nNUMBER_OF_TEMPLATES];
      // this is not used in the case of primers for whole clone reads--it
      // just contains NULLs
} primerType;   



#endif