/*****************************************************************************
#   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    "createUnalignedHighQualityNavigator.h"
#include    "guiMultiContigNavigator.h"
#include    "contig.h"
#include    "locatedFragment.h"
#include    "consedParameters.h"
#include    "rwcregexp.h"
#include    <cstdio>
using namespace std;
#include    "rwtvalvector.h"
#include    "numutil.h"
#include    "contigwin.h"
#include    "unalignedHighQualityRegionsGotoList.h"




void createUnalignedHighQualityNavigator( Widget widTopLevelWidget,
                                          Contig* pContig,
                                          ContigWin* pContigWin ) {


   gotoList* pUnalignedHighQualityRegionsGotoList =
         new unalignedHighQualityRegionsGotoList( pContig,
                                                  true ); // include totally
                                                          // unaligned reads


   RWCString soColumnHeadings1 = "Contig      Read                  Start End     Length";
   RWCString soColumnHeadings2 = "                                  Pos   Pos     ";

   pContigWin->pGuiMultiContigNav_ = 
      new guiMultiContigNavigator(
                                  "Unaligned High Quality Regions",
                                  soColumnHeadings1,
                                  soColumnHeadings2,
                                  100,
                                  "", // extra button
                                  NULL, // extra button
                                  NULL,  // extra button
                                  widTopLevelWidget,
                                  pUnalignedHighQualityRegionsGotoList, // pGotoList
                                  pContigWin
                                  );





   
   pContigWin->pGuiMultiContigNav_->displayList( true );

}