/*****************************************************************************
#   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 arrayOfRestrictionFragments_included
#define arrayOfRestrictionFragments_included

#include    "rwtptrorderedvector.h"
#include    "mbt_exception.h"
#include    "restrictionFragment.h"


class arrayOfRestrictionFragments : 
   public RWTPtrOrderedVector<restrictionFragment> {
public:
   arrayOfRestrictionFragments( size_t sizee = 64 ) :
      RWTPtrOrderedVector<restrictionFragment>( sizee ){}
   

   static int cmpFragmentsBySize( const restrictionFragment** ppFrag1,
                                  const restrictionFragment** ppFrag2 ) {

      if ( (*ppFrag1)->nSize_ < (*ppFrag2)->nSize_ )
         return( 1 );
      else if ( (*ppFrag1)->nSize_ == (*ppFrag2)->nSize_ )
         return( 0 );
      else
         return( -1 );
   }
     

   void sortFragmentsBySize() {
      void* pArray = (void*) data();
      size_t nNumberOfElements = entries();
      size_t nSizeOfAnElement = sizeof( restrictionFragment* );

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

      if ( !bIsSortedBySize() ) {
         THROW_ERROR( "arrayOfRestrictionFragments::sortFragmentsBySize() didn't work" );
      }
   }

   bool bIsSortedBySize() {

      int nNumberOfEntries = entries();
      bool bSorted = true;

      if ( nNumberOfEntries >= 2 ) {
         
         for( int nFrag = 0; nFrag <= nNumberOfEntries - 2;
              ++nFrag ) {
            if ( 
                ( operator[]( nFrag + 1 ))->nSize_ >
                ( operator[]( nFrag ) )->nSize_ 
                ) {
               bSorted = false;
               cerr << "Fragments " << nFrag << " with size " <<
                  ( operator[]( nFrag))->nSize_ << 
                    " and " << nFrag + 1 << " with size " <<
                    ( operator[]( nFrag + 1))->nSize_ <<
                    " are out of order" << endl;
            }
         }
      }

      return( bSorted );
   } //    bool bIsSorted2() {




   static int cmpFragmentsByPosition( const restrictionFragment** ppFrag1,
                                      const restrictionFragment** ppFrag2 ) {


      if ( (*ppFrag1)->nPositionOrder_ < (*ppFrag2)->nPositionOrder_ )
         return( -1 );
      else if ( (*ppFrag1)->nPositionOrder_ == (*ppFrag2)->nPositionOrder_ )
         return( 0 );
      else
         return( 1 );
   }



   void sortFragmentsByPosition() {

      void* pArray = (void*) data();
      size_t nNumberOfElements = entries();
      size_t nSizeOfAnElement = sizeof( restrictionFragment* );

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

      if ( !bIsSortedByPosition() ) {
         THROW_ERROR( "arrayOfRestrictionFragments::sortByPosition didn't work" );
      }
   }



   bool bIsSortedByPosition() {

      int nNumberOfEntries = entries();
      bool bSorted = true;

      if ( nNumberOfEntries >= 2 ) {
         
         for( int nFrag = 0; nFrag <= nNumberOfEntries - 2;
              ++nFrag ) {
            
            if ( 
                ( operator[]( nFrag ))->nPositionOrder_  >
                ( operator[]( nFrag + 1 ))->nPositionOrder_ ) {
               bSorted = false;
               cerr << "Fragments " << nFrag << " with nPositionOrder_ " <<
                  ( operator[]( nFrag ))->nPositionOrder_ << 
                  " and " << nFrag + 1 << " with nPositionOrder_ " <<
                  ( operator[]( nFrag + 1 ))->nPositionOrder_ <<
                  " are out of order" << endl;
            }
         }
      }

      return( bSorted );
   }
                    
         
      





};

#endif