/*****************************************************************************
#   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    "guiMultiContigNavigator.h"
#include    "assembly.h"
#include    "tagsGotoList.h"
#include    "guiGetTagType.h"
#include    "consed.h"


void navigateByTagsInAllContigs() {

   guiGetTagType* pGuiGetTagType = new guiGetTagType();

   RWTValOrderedVector<RWCString> aTagTypesSelectedByUser;
   bool bUserPushedCancel;

   pGuiGetTagType->popupBoxAndWaitForUserToSelectMultipleTagTypes(
                        aTagTypesSelectedByUser,
                        bUserPushedCancel );

   delete pGuiGetTagType;

   if ( bUserPushedCancel) return;


   RWCString soColumnHeadings1;
   RWCString soColumnHeadings2;

   tagTypes::pGetTagTypes()->getColumnHeadingsForNavigatorBox(
                                   "",
                                   soColumnHeadings1,
                                   soColumnHeadings2 );

   RWCString soTagTypesSelectedByUser;
   for( int nTagType = 0; nTagType < aTagTypesSelectedByUser.length(); 
        ++nTagType ) {
      soTagTypesSelectedByUser += aTagTypesSelectedByUser[ nTagType ];
      soTagTypesSelectedByUser += " ";
   }

   
   soTagTypesSelectedByUser = soTagTypesSelectedByUser.soPadOrTruncate( 20 );


   guiMultiContigNavigator* pGuiMultiContigNav = 
      new guiMultiContigNavigator( soTagTypesSelectedByUser + " tags in all contigs",
                                   soColumnHeadings1,
                                   soColumnHeadings2,
                                   100, // width in chars
                                   "",    // special purpose button
                                   NULL,  // special purpose button
                                   NULL,  // special purpose button
                                   NULL,  // parent is GuiApp top level shell
                                   NULL,  // pGotoList
                                   NULL ); // pContigWin


   ConsEd::pGetConsEd()->addGuiMultiContigNavigator( pGuiMultiContigNav );

   Assembly* pAssembly = ConsEd::pGetAssembly();

   for( int nContig = 0; nContig < pAssembly->nNumContigs(); ++nContig ) {
      Contig* pContig = pAssembly->pGetContig( nContig );

      for( int nTagType = 0; nTagType < aTagTypesSelectedByUser.length();
           ++nTagType ) {

         RWCString soOneTagTypeSelectedByUser = 
            aTagTypesSelectedByUser[ nTagType ];


         tagsGotoList* pGotoList = 
            new tagsGotoList( pContig, soOneTagTypeSelectedByUser );

         for( int nGotoItem = 0; nGotoItem < pGotoList->nGetNumGotoItems();
              ++nGotoItem ) {
            gotoItem* pGotoItem = pGotoList->pGetGotoItem( nGotoItem );
            pGuiMultiContigNav->appendToList( pGotoItem );
         }
      } //  for( int nTagType = 0;
   }

   pGuiMultiContigNav->displayList( false );  // don't resort

}