/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef readsSortedByLeftEndPosition_included
#define readsSortedByLeftEndPosition_included

#include    "rwtptrorderedvector.h"
#include    "locatedFragment.h"



class readsSortedByLeftEndPosition : 
   public RWTPtrOrderedVector<LocatedFragment> {
public:
   bool bIsSorted_;


public:

   readsSortedByLeftEndPosition() :
      RWTPtrOrderedVector<LocatedFragment>(), bIsSorted_( false ) {}

   static int cmp( const LocatedFragment** ppLocFrag1,
                   const LocatedFragment** ppLocFrag2 ) {

      if ( (*ppLocFrag1)->nAlignStartPos_ < 
           (*ppLocFrag2)->nAlignStartPos_ )
         return( -1 );
      else if ( (*ppLocFrag1)->nAlignStartPos_ >
                (*ppLocFrag2)->nAlignStartPos_ )
         return( 1 );
      else {
         // reads start at same location.  I think I don't care
         // which is put first

         return( 0 );
      }
   }

   void resort() {
      void* pArray = (void*) data();
      size_t nNumberOfElements = entries();
      size_t nSizeOfAnElement = sizeof( LocatedFragment* );

      qsort( pArray, nNumberOfElements, nSizeOfAnElement,
             ( ( int(*) ( const void*, const void* ) ) cmp ) );

      if ( !bIsSorted() ) {
         THROW_ERROR( "reads out of order" );
      }
   }


   bool bIsSorted() {

      bool bSorted = true;
      for( int nRead = 1; nRead < length(); ++nRead ) {
         
         if (
             ( operator[]( nRead - 1 ) )->nAlignStartPos_ >
             ( operator[]( nRead ) )->nAlignStartPos_
             ) {

            bSorted = false;

            LocatedFragment* pLocFrag1 = operator[]( nRead - 1 );
            LocatedFragment* pLocFrag2 = operator[]( nRead );

            cerr << "Elements " << nRead - 1 << " (" <<
               pLocFrag1->soGetName() << ") and " << nRead <<
               " (" << pLocFrag2->soGetName() << ") are out of order" << endl;
         }
      } //  for( int nRead = 1; ...

      return( bSorted );
   }

   inline void insert( LocatedFragment* pLocFrag ) {
      RWTPtrOrderedVector<LocatedFragment>::insert( pLocFrag );
      bIsSorted_ = false;
   }

   int nFindIndexOfMatchOrPredecessor( const int nMatch ) const {

      if ( isEmpty() ) 
         return( RW_NPOS );

      // region A
      // ----------- nMinIndex
      // region B
      // ----------- nTestIndex
      // region C
      // ----------- nTooLargeIndex 
      // region D

      // an index becomes nTooLargeIndex if it is greater than nMatch
      // an index becomes nMinIndex if it is less than nMatch

      if ( nMatch < operator[]( 0 )->nAlignStartPos_ )
         return( RW_NPOS );

      int nMinIndex = 0;
      int nTooBigIndex = length() - 1;

      if ( operator[]( nTooBigIndex )->nAlignStartPos_ <= nMatch )
         return( nTooBigIndex );

      // if reached here, nMatch < operator[]( nTooBigIndex )
      // and operator[](0) <= nMatch
      // Thus nTooBigIndex != 0  and the correct index is somewhere
      // less than nTooBigIndex and correct index >= 0 so 
      // correct index >= 0.
      // Thus bisect this range over and over, making it smaller
      // and smaller until it is 0.

      while( true ) {
         if ( nTooBigIndex - nMinIndex <= 1 )
            return( nMinIndex );
         else {
            int nTestIndex = ( nTooBigIndex + nMinIndex ) / 2;
            if ( nMatch < operator[]( nTestIndex )->nAlignStartPos_ )
               nTooBigIndex = nTestIndex;
            else
               nMinIndex = nTestIndex;
         }
      }
   }
   
   // written Jan 2008
   int nFindIndexOfMatchOrSuccessor( const int nConsPos ) const {

      if ( isEmpty() )
         return( RW_NPOS );

      // region A
      // ----------- nTooSmallIndex
      // region B
      // ----------- nTestIndex
      // region C
      // ----------- nMaxIndex
      // region D

      // an index becomes nMaxIndex if it is greater than nMatch
      // an index becomes nTooSmallIndex if it is less than nMatch

      int nTooSmallIndex = 0;
      int nMaxIndex = length() - 1;

      if ( operator[]( nMaxIndex )->nAlignStartPos_ < nConsPos )
         return( RW_NPOS );

      // if reached here,  nConsPos <= operator[]( nMaxIndex)->nAlignStartPos_

      if ( nConsPos <= operator[]( nTooSmallIndex )->nAlignStartPos_ )
         return( nTooSmallIndex );

      // if reached here, 
      // operator[]( nTooSmallIndex)->nAlignStartPos_ < 
      //      nConsPos <=
      // operator[]( nMaxIndex )->nAlignStartPos_
      // Thus the names nTooSmallIndex and nMaxIndex apply.
      
      while( true ) {

         if ( nMaxIndex - nTooSmallIndex <= 1 )
            return( nMaxIndex );
         else {
            int nTestIndex = ( nTooSmallIndex + nMaxIndex ) / 2;
            if ( operator[]( nTestIndex )->nAlignStartPos_ < nConsPos )
               nTooSmallIndex = nTestIndex;
            else 
               nMaxIndex = nTestIndex;
         }
      }
   }
      
};




#endif