/*****************************************************************************
#   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    "sortAcceptablePrimers.h"
#include    <stdlib.h>
#include    <iostream.h>



// put acceptable first, then unacceptable
// within acceptable, put closest to cursor first
// within same distance to cursor, put shortest primers first

static int nSortByAcceptableAndPosition( const primerType* pPrimer2,
                                         const primerType* pPrimer1 ) {

   if ( !pPrimer1->bAcceptable_ && !pPrimer2->bAcceptable_ )
      return( 0 );

   else if ( !pPrimer1->bAcceptable_ && pPrimer2->bAcceptable_ )
      return( -1 );

   else if ( pPrimer1->bAcceptable_ && !pPrimer2->bAcceptable_ )
      return( 1 );

   else {
      // ( pPrimer1->bAcceptable_ && pPrimer2->bAcceptable ) {

      if ( pPrimer1->nDistanceFromCursor_ < pPrimer2->nDistanceFromCursor_ )
         return( 1 );
      else if ( pPrimer1->nDistanceFromCursor_ > pPrimer2->nDistanceFromCursor_ )
         return( -1 );
      else {
         if ( pPrimer1->nUnpaddedLength_ < pPrimer2->nUnpaddedLength_ )
            return( 1 );
         else if ( pPrimer1->nUnpaddedLength_ > pPrimer2->nUnpaddedLength_ )
            return( -1 );
         else
            return( 0 );
      }
   }
}


static void checkIfSorted( primerType* pPrimerArray, 
                           const int nNumberOfPrimers ) {

   int nDistanceFromCursorLastPrimer;

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

      primerType* pPrimer = pPrimerArray + nPrimer;
      if ( !pPrimer->bAcceptable_ ) continue;

      if ( nPrimer != 0 ) {
         if ( ! ( nDistanceFromCursorLastPrimer <= pPrimer->nDistanceFromCursor_  ) ) {
            cout << "problem: primers out of order " << nPrimer << 
               " old dist " << nDistanceFromCursorLastPrimer <<
               " new dist " << pPrimer->nDistanceFromCursor_ << endl;
         }
      }
      nDistanceFromCursorLastPrimer = pPrimer->nDistanceFromCursor_;
   }  

}




void sortAcceptablePrimers( primerType* pPrimerArray, 
                            const int nNumberOfPrimers,
                            const bool bForwardNotReversePrimers ) {

   void* pArray = (void*) pPrimerArray;

   size_t nNumberOfElementsInArray = nNumberOfPrimers;
   size_t nSizeOfAnElement = sizeof( primerType );

   qsort( pArray, nNumberOfElementsInArray, nSizeOfAnElement,
          ( ( int(*) ( const void*, const void* ) ) nSortByAcceptableAndPosition ) );

   checkIfSorted( pPrimerArray, nNumberOfPrimers );

}