/*****************************************************************************
#   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    "regionOfSequenceArray.h"
#include    "bIntervalsIntersect.h"
#include    "consedParameters.h"


regionOfSequence* regionOfSequenceArray :: pGetOverlappingRegion( 
                 regionOfSequence* pRegionOfSequenceQuery ) {

   int nIndex = nFindIndexOfMatchOrPredecessor( pRegionOfSequenceQuery );


   if ( nIndex == RW_NPOS ) 
      return NULL;

   int nWantedIndex = -666;
   bool bWantThisAlignment = false;
   bool bContinue = true;
   while( bContinue ) {
      if ( ( nIndex == RW_NPOS ) || ( nIndex >= length() ) ) {
         bContinue = false;
      }
      else {
         if ( (*this)[ nIndex ]->soSequenceName_ == 
              pRegionOfSequenceQuery->soSequenceName_ ) {
            
            if ( bIntervalsIntersect( (*this)[ nIndex ]->n1StartPos_,
                                      (*this)[ nIndex ]->n1EndPos_,
                                      pRegionOfSequenceQuery->n1StartPos_,
                                      pRegionOfSequenceQuery->n1EndPos_ ) ) {
               bWantThisAlignment = true;
               bContinue = false;
               nWantedIndex = nIndex;
            }
            else if ( pRegionOfSequenceQuery->n1EndPos_ <
                      (*this)[ nIndex ]->n1StartPos_ ) {

               // we are now into region that are to the right of the 
               // alignment

               bContinue = false;
            }
         }
         else {
            // different sequence
            
            if ( pRegionOfSequenceQuery->soSequenceName_ <
                 (*this)[ nIndex ]->soSequenceName_ ) {
               // we are past the sequence we are interested in
               bContinue = true;
            }
         }
      }

      ++nIndex;
   } //  while( bContinue ) {

   if ( bWantThisAlignment ) {
      return (*this)[ nWantedIndex ];
   }
   else
      return NULL;
}