/*****************************************************************************
#   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    "contig.h"
#include    "primerType.h"
#include    "consedParameters.h"
#include    "numutil.h"
#include    <cstdlib>  // for malloc
using namespace std;
#include    "createPrimerCandidate.h"

void   createPrimerCandidates( Contig* pContigOfCursor, 
                               const int nPaddedConsPosOfCursor,
                               const bool bForwardNotReversePrimer,
                               primerType** ppPrimerArray,
                               int& nNumberOfPrimers ) {

   
   int nUnpaddedPosOfCursor = pContigOfCursor->nUnpaddedIndex( nPaddedConsPosOfCursor );

   int nMinUnpadded;
   int nMaxUnpadded;

   if (bForwardNotReversePrimer ) {
      nMaxUnpadded = nUnpaddedPosOfCursor - 
         consedParameters::pGetConsedParameters()->nPrimersNumberOfBasesToBackUpToStartLooking_;
      
      if (nMaxUnpadded < pContigOfCursor->nGetUnpaddedStartIndex() ) {
         cout << "can't back up " << consedParameters::pGetConsedParameters()->nPrimersNumberOfBasesToBackUpToStartLooking_ << 
            " so not backing up" << endl;

         nMaxUnpadded = nUnpaddedPosOfCursor;
      }

      nMinUnpadded = nMaxUnpadded - 
       consedParameters::pGetConsedParameters()->nPrimersWindowSizeInLookingToUse_;

      nMinUnpadded = MAX( nMinUnpadded, pContigOfCursor->nGetUnpaddedStartIndex() );

   }
   else {
      nMinUnpadded =  nUnpaddedPosOfCursor +
         consedParameters::pGetConsedParameters()->nPrimersNumberOfBasesToBackUpToStartLooking_;

      if (nMinUnpadded + consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_ > pContigOfCursor->nGetUnpaddedEndIndex() ) {
         cout << "can't move to the right " <<
            consedParameters::pGetConsedParameters()->nPrimersNumberOfBasesToBackUpToStartLooking_ <<
            " so not moving to right" << endl;
            
         nMinUnpadded = nUnpaddedPosOfCursor;
      }

      nMaxUnpadded = nMinUnpadded +
        consedParameters::pGetConsedParameters()->nPrimersWindowSizeInLookingToUse_;

      nMaxUnpadded = MIN( nMaxUnpadded, 
                          pContigOfCursor->nGetUnpaddedEndIndex()
                          );
   } 


   if ( ! (
           ( nMinUnpadded <= nMaxUnpadded ) &&
           ( pContigOfCursor->nGetUnpaddedStartIndex() <= nMinUnpadded ) &&
           ( nMaxUnpadded <= pContigOfCursor->nGetUnpaddedEndIndex() )
           ) ) {
      cerr << "nMinUnpadded = " << nMinUnpadded << endl;
      cerr << "nMaxUnpadded = " << nMaxUnpadded << endl;
      cerr << "nUnpaddedPosOfCursor = " << nUnpaddedPosOfCursor << endl;
      cerr << "nPaddedPosOfCursor = " << nPaddedConsPosOfCursor << endl;
      cerr << "pContigOfCursor->nGetUnpaddedStartIndex() = " <<
         pContigOfCursor->nGetUnpaddedStartIndex() << endl;
      cerr << "pContigOfCursor->nGetUnpaddedEndIndex() = " <<
         pContigOfCursor->nGetUnpaddedEndIndex() << endl;
      cerr << "bForwardNotReversePrimer = " << 
         ( bForwardNotReversePrimer ? "true" : "false" ) << endl;

      assert( false );
   }

   assert( nMinUnpadded <= nMaxUnpadded );
   assert( pContigOfCursor->nGetUnpaddedStartIndex() <= nMinUnpadded );
   assert( nMaxUnpadded <= pContigOfCursor->nGetUnpaddedEndIndex() );

   int nUnpaddedPositionsForPrimersToStart = nMaxUnpadded - nMinUnpadded + 1;
   nNumberOfPrimers = nUnpaddedPositionsForPrimersToStart *
      ( consedParameters::pGetConsedParameters()->nPrimersMaximumLengthOfAPrimerToUse_
        -
        consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_
        + 1 );

   primerType* pPrimerArray = (primerType*) malloc( sizeof( primerType ) 
                                      * nNumberOfPrimers );

   //   cerr << "allocating " << sizeof( primerType ) * nNumberOfPrimers << 
   //      " bytes" << endl;
   
   assert( pPrimerArray );
   *ppPrimerArray = pPrimerArray;  // value to return

   int nPrimersSoFar = 0;
   for( int nUnpadded = nMinUnpadded; nUnpadded <= nMaxUnpadded; 
        ++nUnpadded ) {
      for( int nLengthOfPrimer = 
   consedParameters::pGetConsedParameters()->nPrimersMinimumLengthOfAPrimerToUse_;
              nLengthOfPrimer <= 
   consedParameters::pGetConsedParameters()->nPrimersMaximumLengthOfAPrimerToUse_;
              ++nLengthOfPrimer ) {

         // for every end position, there must be a shortest primer
         // in order to do the matches to template and vector.
         // thus make sure there is a shortest primer ending at
         // nMaxUnpadded

         if ( nUnpadded + nLengthOfPrimer - 1 > nMaxUnpadded )
            continue;
    
         primerType* pPrimer = pPrimerArray + nPrimersSoFar;

         createPrimerCandidate( pPrimer, nUnpadded, nLengthOfPrimer,
                          bForwardNotReversePrimer,
                          pContigOfCursor, nUnpaddedPosOfCursor );

         ++nPrimersSoFar;

      }
   }

   assert( nPrimersSoFar <= nNumberOfPrimers );
   nNumberOfPrimers = nPrimersSoFar;

}