/*****************************************************************************
#   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    "gotoListType.h"
#include    <Xm/Xm.h>
#include    "contig.h"
#include    "multiProblemGotoList.h"
#include    "gotoList.h"
#include    "lowconsqual.h"
#include    "highQualityDiscrepancyGotoList.h"
#include    "singleSubcloneRegionsGotoList.h"
#include    "unalignedHighQualityRegionsGotoList.h"
#include    "singleStrandedRegionsGotoList.h"



multiProblemGotoList :: multiProblemGotoList( gotoListType gotoListTypes,
                                      Contig* pContig ) {

   if ( ( lowConsensusQualityType & gotoListTypes ) ) {
      
      gotoList* pLowConsQualGotoList = new LowConsQualGotoList( pContig );
      appendAnotherList( pLowConsQualGotoList );
      
      delete pLowConsQualGotoList;

   }

   if ( ( highQualityDiscrepancyType & gotoListTypes ) ) {

      gotoList* pHighQualityDiscrepanciesGotoList =
         new highQualityDiscrepancyGotoList( pContig, false, false );

      appendAnotherList( pHighQualityDiscrepanciesGotoList );

      delete pHighQualityDiscrepanciesGotoList;
   }

   if ( ( highQualityDiscrepancyWithoutCompressionsAndG_dropoutsType 
          & gotoListTypes ) ) {
      
      gotoList* pHighQualityDiscrepanciesGotoList =
         new highQualityDiscrepancyGotoList( pContig, true, false );

      appendAnotherList( pHighQualityDiscrepanciesGotoList );

      delete pHighQualityDiscrepanciesGotoList;
   }

   if ( singleStrandedRegionsType &
        gotoListTypes ) {

      gotoList* pSingleStrandedRegionsGotoList =
         new singleStrandedRegionsGotoList( pContig );

      appendAnotherList( pSingleStrandedRegionsGotoList );
      
      delete pSingleStrandedRegionsGotoList;
   }

   if ( singleSubcloneRegionsType &
        gotoListTypes ) {

      gotoList* pSingleSubcloneRegionsGotoList =
         new singleSubcloneRegionsGotoList( pContig );

      appendAnotherList( pSingleSubcloneRegionsGotoList );

      delete pSingleSubcloneRegionsGotoList;
   }

   if ( unalignedHighQualityRegionsType & gotoListTypes ) {

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


      appendAnotherList( pUnalignedHighQualityRegionsGotoList );
      delete pUnalignedHighQualityRegionsGotoList;
   }

   sortByPosition();
}