/*****************************************************************************
#   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.
#
#*****************************************************************************/
#include    "pickPCRPrimersForOneEndOfContig.h"
#include    "primerType.h"
#include    "contig.h"
#include    "consedParameters.h"
#include    "fileDefines.h"
#include    "createPrimerCandidates.h"
#include    "findPrimerMatchesElsewhere.h"
#include    "findPrimerSelfMatches.h"
#include    "whichPrimersAreAcceptable.h"
#include    "findPrimerMatchesAgainstSequencesInFile.h"
#include    "copyPrimerMatchesFromShorterToLongerPrimers.h"
#include    "calculatePrimerMeltingTemperatures.h"
#include    "checkPrimersForMononucleotideRepeats.h"
#include    "checkPrimersForACGT.h"



void pickPCRPrimersForOneEndOfContig(
         primerType*& pPrimerArray,
         int& nPrimersInPrimerArray,
         Contig* pContig,
         const int nWhichEnd,
         int& nNumberOfAcceptablePrimers ) {



   pCP->setParametersForSequencingPrimersNotPCRPrimers( false );


   // go back 100 bases from the end of the high quality segment

   pCP->nPrimersNumberOfBasesToBackUpToStartLooking_ = 0;

   int nConsPos = pContig->nGetPaddedConsPosForMakingPCRPrimers( nWhichEnd );

   bool bTopStrandPCRPrimer = ( nWhichEnd == nRightGap ? true : false );

   createPrimerCandidates( pContig,
                           nConsPos,
                           bTopStrandPCRPrimer,
                           &pPrimerArray,
                           nPrimersInPrimerArray );

   findPrimerMatchesElsewhere( pPrimerArray,
                               nPrimersInPrimerArray,
                               bTopStrandPCRPrimer,
                               true ); // bCloneNotSubcloneTemplate


   if ( pCP->bPrimersScreenForVector_ ) {
      findPrimerMatchesAgainstSequencesInFile( pPrimerArray,
                                               nPrimersInPrimerArray,
                                               true ); // bCloneNotSubcloneTemplate
   }


   copyPrimerMatchesFromShorterToLongerPrimers( pPrimerArray,
                                                nPrimersInPrimerArray,
                                                bTopStrandPCRPrimer );

   calculatePrimerMeltingTemperatures( pPrimerArray,
                                       nPrimersInPrimerArray );

   findPrimerSelfMatches( pPrimerArray, nPrimersInPrimerArray );


   checkPrimersForMononucleotideRepeats( pPrimerArray,
                                         nPrimersInPrimerArray,
                                         nNumberOfAcceptablePrimers );

   checkPrimersForACGT( pPrimerArray,
                        nPrimersInPrimerArray,
                        nNumberOfAcceptablePrimers );

   whichPrimersAreAcceptable( pPrimerArray,
                              nPrimersInPrimerArray,
                              nNumberOfAcceptablePrimers );

   fprintf( pAO, "%d acceptable primers on %s end of contig %s\n",
            nNumberOfAcceptablePrimers,
            ( nWhichEnd == nLeftGap ? "left" : "right" ),
            pContig->soGetName().data() );

}