/*****************************************************************************
#   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    "consedParameters.h"
#include    "whichPrimersHaveAcceptableMeltingTemp.h"
#include    "primerType.h"
#include    "dGetPrimerMeltingTemperature.h"
#include    "whyIsPrimerNotAcceptableTypes.h"


void whichPrimersHaveAcceptableMeltingTemp( primerType* pPrimerArray,
                                            const int nNumberOfPrimers,
                                            bool& bSomeAcceptablePrimers ) {

   bSomeAcceptablePrimers = false;

   double dMinTemp = (double) consedParameters::pGetConsedParameters()->nPrimersMinMeltingTempToUse_;

   double dMaxTemp = (double) consedParameters::pGetConsedParameters()->nPrimersMaxMeltingTempToUse_;


   for( int nPrimer = 0; nPrimer < nNumberOfPrimers; ++nPrimer ) {

      primerType* pPrimer = pPrimerArray + nPrimer;

      if (! pPrimer->bAcceptable_ ) continue;

      pPrimer->dMeltingTemperature_ = dGetPrimerMeltingTemperature(
                                            pPrimer->szPrimer_,
                                            pPrimer->nUnpaddedLength_ );

      if ( ( dMinTemp <= pPrimer->dMeltingTemperature_  ) &&
           ( pPrimer->dMeltingTemperature_ <= dMaxTemp ) 
            ) 
         bSomeAcceptablePrimers = true;
      else {
         pPrimer->bAcceptable_ = false;

	 if ( pPrimer->dMeltingTemperature_ < dMinTemp )
	   pPrimer->nWhyIsPrimerNotAcceptable_ = 
	     BAD_PRIMER_MELTING_TEMPERATURE_TOO_LOW;
	 else
	   pPrimer->nWhyIsPrimerNotAcceptable_ =
	     BAD_PRIMER_MELTING_TEMPERATURE_TOO_HIGH;

      }
   }
 


}