/*****************************************************************************
#   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 clScaffold_included
#define clScaffold_included

#include    "rwtptrorderedvector.h"
#include    "rwtvalorderedvector.h"

class contigEndPair;
class Contig;

// seems that this is just a temporary structure to be created
// in order to cut up the scaffold into digest fragments and then
// deleted.  The permanent structures are held in the Assembly object
// (e.g., aHeadsOfScaffoldsOfContigs_ which are just Contigs)
// and the Contig objects ( pPreviousContig_, pNextContig_, etc )

class clScaffold {
public:
   // all of the below must be precisely the same length
   RWTPtrOrderedVector<Contig> aContigs_;
   RWTValOrderedVector<bool> aIfContigsAreComplemented_;

   // Note that there is one fewer of these
   // than the two arrays above.
   RWTPtrOrderedVector<contigEndPair> aContigEndPairs_;

   bool bFirstContigIsCloneEnd_;
   bool bLastContigIsCloneEnd_;

   // these are only used in the case of contigs maps
   // for subclones
   bool bUseFirstContigUnpaddedStart_;
   bool bUseLastContigUnpaddedEnd_;
   int nFirstContigUnpaddedStart_;
   int nLastContigUnpaddedEnd_;

   // this is not always filled in.  It is filled in if the scaffold
   // is gotten via Assembly::getScaffolds
   int nScaffoldLength_;

   const int nScaffold_; // index in Assembly::aHadsOfScaffoldsOfContigs_

   int nScaffoldRow_;
   int nScaffoldOnScaffoldRow_;
   int nScaffoldPositionsBeforeItOnScaffoldRow_;

public:
   clScaffold( const int nScaffold ) : 
      nScaffold_( nScaffold ),
      bFirstContigIsCloneEnd_( false ),
      bLastContigIsCloneEnd_( false ),
      bUseFirstContigUnpaddedStart_( false ),
      bUseLastContigUnpaddedEnd_( false ) {}

   bool operator==( const clScaffold& scaf ) const {
      if ( this == &scaf )
         return( true );
      else
         return( false );
   }

   void setScaffoldLength();

   RWCString soGetDescription();

   void fixOrientation( RWCString& soErrorMessage );
   void removeTheCs();
   void flipScaffold();
   void unfixOrientation();

};   


#endif