/*****************************************************************************
#   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    <Xm/Xm.h>
#include    <Xm/SelectioB.h>
#include    <iostream>
using namespace std;
#include    <Xm/Form.h>
#include    <Xm/PushB.h>
#include    <Xm/MainW.h>
#include    <Xm/List.h>

#include    "assert.h"
#include    "contigwin.h"
#include    "consed.h"
#include    "guicontigwin.h"
#include    "guiMultiContigNavigator.h"
#include    "handleWindowManagerDelete.h"
#include    "consedParameters.h"
#include    "hp_exception_kludge.h"
#include    "assemblyView.h"




guiMultiContigNavigator :: guiMultiContigNavigator(
                               const RWCString& soWindowTitle,
                               const RWCString& soTextForFirstLine,
                               const RWCString& soTextForSecondLine,
                               const int nWidthInChars,
                               const RWCString& soTitleOfSpecialPurposeButton,
                               cbSpecialPurposeButton cbS,
                               void* pClientDataForCbSpecialPurposeButton,
                               Widget widTopLevelShellToBeConnectedTo,
                               gotoList* pGotoList,
                               ContigWin* pContigWin,
                               const RWCString& soTextForThirdLine
                               ) :
   pcbSpecialPurposeButton_( cbS ),
   pClientDataForSpecialPurposeButton_( pClientDataForCbSpecialPurposeButton ),
   pContigWin_( pContigWin ),
   pAssemblyView_( NULL )
{


   // activating prev/next buttons on all traces window
   if ( pContigWin_ )
      pContigWin_->pGuiMultiContigNav_ = this;



   if ( ! pGotoList ) 
      pGotoList_ = new gotoList( );
   else
      pGotoList_ = pGotoList;
      


   int nArgs;
   Arg aArg[500];


   // set private member indicating current selection
   // to be const value for no selection
   nCurrentSelection_ = navigatorNoSelection;

   // how many GotoItems in the list?
   int nNumGotoItems = pGotoList_->nGetNumGotoItems();

   // allocate space for the array of XmStrings
   XmString* paXms;  // pointer to array
   if (nNumGotoItems > 0 )
      paXms = new XmString[nNumGotoItems];
   else {
      paXms = NULL;
   }

   // populate the array of XmStrings for the listbox resource
   int n;
   for( n = 0; n < nNumGotoItems; n++) {
      paXms[n] = 
        // get char* from GotoItem* from GotoList*
        XmStringCreateSimple((char*)(*pGotoList_)[n]->soGetFullDesc().data());
   }

   // the list box title is from the GotoList's description
   XmString xmsListLabel = 
     XmStringCreateSimple( (char*) soWindowTitle.data() );

   XmString xmsSelectionLabel = XmStringCreateSimple("Go to");

   bool bParentIsTopLevelWindow = false;
   if (widTopLevelShellToBeConnectedTo == NULL ) {
      bParentIsTopLevelWindow = true;
      widTopLevelShellToBeConnectedTo = GuiApp::pGetGuiApp()->widGetTopLevel();
   }


   // figure out where to place the box on the screen
   // Place it right below the window that is calling this one.

   Dimension nHeight;
   Dimension nWidth;
   Position nY;
   Position nX;


   XtVaGetValues( widTopLevelShellToBeConnectedTo,
                  XmNheight, &nHeight, 
                  XmNwidth,  &nWidth,
                  XmNy, &nY,
                  XmNx, &nX,
                  NULL );

   if ( bParentIsTopLevelWindow ) {
      widPopupShell_ = XtVaCreatePopupShell(
                             "consed",
                             topLevelShellWidgetClass,
                             widTopLevelShellToBeConnectedTo,
                             XmNtitle, (char*) soWindowTitle.data(),
                             XmNnoResize, False,
                             XmNautoUnmanage, False,
                             XmNtransient, False,
                             XmNdeleteResponse, XmDO_NOTHING,
                             NULL );
   }
   else {
      widPopupShell_ = XtVaCreatePopupShell(
                             "consed",
                             topLevelShellWidgetClass,
                             widTopLevelShellToBeConnectedTo,
                             XmNtitle, (char*) soWindowTitle.data(),
                             XmNnoResize, False,
                             XmNautoUnmanage, False,
                             XmNtransient, False,
                             XmNdeleteResponse, XmDO_NOTHING,
                             XmNy, nY + nHeight,
                             XmNx, nX,
                             NULL );
   }
   

   handleWindowManagerDelete( widPopupShell_ );


   // the immediate child of the application shell is a
   // main window
   Widget widMainWin = 
     XtVaCreateManagedWidget("mainwin", 
                             xmMainWindowWidgetClass, widPopupShell_,
                             XmNancestorSensitive, True,  
                             NULL );

   //
   // create the form widget
   //
   nArgs = 0;
   XtSetArg(aArg[nArgs],XmNshadowThickness,0); nArgs++;
   XtSetArg(aArg[nArgs],XmNborderWidth,0); nArgs++;
   Widget widForm = XmCreateForm(widMainWin,
                           "form",
                           aArg,
                           nArgs);
   XtManageChild(widForm);

   RWCString soTextToDisplay;
   short shRows;

   if ( soTextForThirdLine.bIsNull() ) {

      soTextToDisplay = soTextForFirstLine + "\n" +
         soTextForSecondLine;

      shRows = 2;
   }
   else {

      soTextToDisplay = soTextForFirstLine + "\n" +
         soTextForSecondLine + "\n" +
         soTextForThirdLine;

      shRows = 3;
   }


   nArgs = 0;
   XtSetArg(aArg[nArgs], XmNeditable, false); nArgs++;
   XtSetArg(aArg[nArgs], XmNcursorPositionVisible, false); nArgs++;
   XtSetArg(aArg[nArgs], XmNrows, shRows ); nArgs++;
   XtSetArg(aArg[nArgs], XmNtraversalOn, False); nArgs++;
   XtSetArg(aArg[nArgs], XmNvalue, (char*) soTextToDisplay.data()); nArgs++;
   XtSetArg(aArg[nArgs], XmNtopAttachment, XmATTACH_FORM); nArgs++;
   XtSetArg(aArg[nArgs], XmNtopOffset, 0); nArgs++;
   XtSetArg(aArg[nArgs], XmNleftAttachment, XmATTACH_FORM); nArgs++;
   XtSetArg(aArg[nArgs], XmNrightAttachment, XmATTACH_FORM); nArgs++;
   XtSetArg( aArg[nArgs], XmNeditMode, XmMULTI_LINE_EDIT ); ++nArgs;
   XtSetArg( aArg[nArgs], XmNcolumns, nWidthInChars ); ++nArgs;
   // removing this method of setting fontList to fix SuSe bug 
   // that gives dagger characters
   //   XtSetArg( aArg[nArgs], XmNfontList, GuiApp::pGetGuiApp()->xmfontListGet() ); ++nArgs;
   widFirstLineText_ = XmCreateText(widForm, "navtextfield", aArg, nArgs);


   XtManageChild(widFirstLineText_);


   const int nSpacingBetweenButtons = 1;

   int nButtonLocationLeft[6];
   int nButtonLocationRight[6];

   
   bool bAddMultiplePurposeButton = ( pcbSpecialPurposeButton_ ) ? true : false;

   int nNumberOfButtons = bAddMultiplePurposeButton ? 6 : 5;

   double dWidthOfAButton = ( 100 - nSpacingBetweenButtons * ( nNumberOfButtons + 1) ) /
      (double) nNumberOfButtons;

   for( int nButton = 0; nButton < nNumberOfButtons; ++nButton ) {
      nButtonLocationLeft[ nButton ] = 
         nSpacingBetweenButtons * ( nButton + 1 ) +
         (int) (dWidthOfAButton * nButton );

      nButtonLocationRight[ nButton ] = 
         nSpacingBetweenButtons * ( nButton + 1 ) +
         (int) (dWidthOfAButton * ( nButton + 1 ));

   }



   // get the widget id's of the buttons (stored in appropriately
   // named members)

   widGoButton_ = XtVaCreateManagedWidget( "Go",
        xmPushButtonWidgetClass,
        widForm,
       XmNbottomAttachment, XmATTACH_FORM,
       XmNbottomOffset, 10,                                           
       XmNtraversalOn, False,
       XmNleftAttachment, XmATTACH_POSITION,
       XmNleftPosition, nButtonLocationLeft[0],
       XmNrightAttachment, XmATTACH_POSITION,
       XmNrightPosition, nButtonLocationRight[0],
       NULL );                                                 


   XtAddCallback(widGoButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);


   widPrevButton_ = XtVaCreateManagedWidget( "Prev",
        xmPushButtonWidgetClass,
        widForm,
       XmNbottomAttachment, XmATTACH_FORM,
       XmNbottomOffset, 10,                                           
       XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET,
       XmNtopWidget, widGoButton_,
       XmNtraversalOn, False,
       XmNleftAttachment, XmATTACH_POSITION,
       XmNleftPosition, nButtonLocationLeft[1],
       XmNrightAttachment, XmATTACH_POSITION,
       XmNrightPosition, nButtonLocationRight[1],
       NULL );                                                 


   XtAddCallback(widPrevButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);


   widNextButton_ = XtVaCreateManagedWidget( "Next",
        xmPushButtonWidgetClass,
        widForm,
       XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET,
       XmNtopWidget, widGoButton_,
       XmNbottomAttachment, XmATTACH_FORM,
       XmNbottomOffset, 10,                                           
       XmNtraversalOn, False,
       XmNleftAttachment, XmATTACH_POSITION,
       XmNleftPosition, nButtonLocationLeft[2],
       XmNrightAttachment, XmATTACH_POSITION,
       XmNrightPosition, nButtonLocationRight[2],
       NULL );                                                 


   XtAddCallback(widNextButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);


   widSaveButton_ = XtVaCreateManagedWidget( "Save",
        xmPushButtonWidgetClass,
        widForm,
       XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET,
       XmNtopWidget, widGoButton_,
       XmNbottomAttachment, XmATTACH_FORM,
       XmNbottomOffset, 10,                                           
       XmNtraversalOn, False,
       XmNleftAttachment, XmATTACH_POSITION,
       XmNleftPosition, nButtonLocationLeft[3],
       XmNrightAttachment, XmATTACH_POSITION,
       XmNrightPosition, nButtonLocationRight[3],
       NULL );                                                 



   XtAddCallback(widSaveButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);

   if ( bAddMultiplePurposeButton ) {

      widSpecialPurposeButton_ = XtVaCreateManagedWidget( 
            (char*) soTitleOfSpecialPurposeButton.data(),
            xmPushButtonWidgetClass,
            widForm,
            XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET,
            XmNtopWidget, widGoButton_,
            XmNbottomAttachment, XmATTACH_FORM,
            XmNbottomOffset, 10,                                           
            XmNtraversalOn, False,
            XmNleftAttachment, XmATTACH_POSITION,
            XmNleftPosition, nButtonLocationLeft[4],
            XmNrightAttachment, XmATTACH_POSITION,
            XmNrightPosition, nButtonLocationRight[4],
            NULL );                                                 


      XtAddCallback(widSpecialPurposeButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);
   }
   else widSpecialPurposeButton_ = NULL;


   int nLastButtonIndex =  bAddMultiplePurposeButton ? 5 : 4;

   widDismissButton_ = XtVaCreateManagedWidget( "Dismiss",
        xmPushButtonWidgetClass,
        widForm,
       XmNtopAttachment, XmATTACH_OPPOSITE_WIDGET,
       XmNtopWidget, widGoButton_,
       XmNbottomAttachment, XmATTACH_FORM,
       XmNbottomOffset, 10,                                           
       XmNtraversalOn, False,
       XmNleftAttachment, XmATTACH_POSITION,
       XmNleftPosition, nButtonLocationLeft[ nLastButtonIndex ],
       XmNrightAttachment, XmATTACH_POSITION,
       XmNrightPosition, nButtonLocationRight[ nLastButtonIndex ],
       NULL );                                                 


   XtAddCallback(widDismissButton_,
                 XmNactivateCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);


   nArgs = 0;
   XtSetArg(aArg[nArgs], XmNselectionPolicy, XmSINGLE_SELECT); nArgs++;
   XtSetArg(aArg[nArgs], XmNmustMatch, True); nArgs++;
   XtSetArg(aArg[nArgs], XmNlistItems, paXms); nArgs++;
   XtSetArg(aArg[nArgs], XmNlistItemCount, nNumGotoItems); nArgs++;
   XtSetArg(aArg[nArgs], XmNlistLabelString, xmsListLabel); nArgs++;
   //   XtSetArg(aArg[nArgs], XmNselectionLabelString, xmsSelectionLabel); nArgs++;
   XtSetArg(aArg[nArgs], XmNdialogType, XmDIALOG_COMMAND); nArgs++;
   XtSetArg(aArg[nArgs], XmNtopAttachment, XmATTACH_WIDGET); nArgs++;
   XtSetArg(aArg[nArgs], XmNtopWidget, widFirstLineText_ ); nArgs++;
   XtSetArg(aArg[nArgs], XmNtopOffset, 0 ); nArgs++;
   XtSetArg(aArg[nArgs], XmNleftAttachment, XmATTACH_FORM); nArgs++;
   XtSetArg(aArg[nArgs], XmNrightAttachment, XmATTACH_FORM); nArgs++;
   XtSetArg(aArg[nArgs], XmNbottomAttachment, XmATTACH_WIDGET); nArgs++;
   XtSetArg(aArg[nArgs], XmNbottomWidget, widGoButton_); nArgs++;
   XtSetArg(aArg[nArgs], XmNbottomOffset, 10 ); nArgs++;
   XtSetArg(aArg[nArgs], XmNmarginWidth, 0 ); nArgs++;
   XtSetArg(aArg[nArgs], XmNmarginHeight, 0 ); nArgs++;
   XtSetArg( aArg[nArgs], XmNtextColumns, (short) nWidthInChars ); ++nArgs;

   widSelectionBox_ = 
     XmCreateSelectionBox( widForm,
                             "navigator",
                             aArg,
                             nArgs);

   XtManageChild( widSelectionBox_ );


   // get the widget id for the text widget
   Widget widText = 
      XmSelectionBoxGetChild(widSelectionBox_, XmDIALOG_TEXT);
   // make the text not editable, traversal off, etc.

   XtUnmanageChild( widText );

   Widget widLabel =
      XmSelectionBoxGetChild(widSelectionBox_, XmDIALOG_SELECTION_LABEL);

   XtUnmanageChild( widLabel );

   // get the widget id for the list widget
   widList_ = 
     XmSelectionBoxGetChild(widSelectionBox_, XmDIALOG_LIST);
   // set traversal off for list, etc.
   nArgs = 0;
   XtSetArg(aArg[nArgs], XmNtraversalOn, False); nArgs++;
   
   // removing this method of setting fontList to fix SuSe bug 
   // that gives dagger characters
   // XtSetArg( aArg[nArgs], XmNfontList, GuiApp::pGetGuiApp()->xmfontListGet() ); ++nArgs;
   //   XtSetArg(aArg[nArgs], XmNlistSizePolicy, XmVARIABLE ); nArgs++;
   XtSetValues(widList_, aArg, nArgs);

   // This is so the user can double-click on an item on the list rather
   // than single clicking and clicking 'go'

   XtAddCallback(widList_,
                 XmNdefaultActionCallback, 
                 (XtCallbackProc )guiMultiContigNavigatorXtButtonCb,
                 this);

   XtManageChild(widSelectionBox_);


   // free the strings we used
   XmStringFree(xmsListLabel);
   XmStringFree(xmsSelectionLabel);
   for (n = 0; n < nNumGotoItems; n++) {
      XmStringFree(paXms[n]);
   }


   XtPopup( widPopupShell_, XtGrabNone );

}


void guiMultiContigNavigatorXtButtonCb(Widget wid,
                         XtPointer clientData,
                         XmSelectionBoxCallbackStruct* cbs) {
   guiMultiContigNavigator* pNav = (guiMultiContigNavigator* )clientData;


   TRY_CATCH_WRAPPER(
   pNav->guiMultiContigNavigatorXtButtonCb2( wid ) 
                     );
}



void guiMultiContigNavigator :: popDownAndDestroy() {
      delete this;
}



void guiMultiContigNavigator :: guiMultiContigNavigatorXtButtonCb2( Widget wid ) {

   // Dismiss button
   if (wid == widDismissButton_ ) {
      popDownAndDestroy();
      return;
   }

   // in all cases except for dismiss, there must be some items in the list.
   // otherwise ignore the user.

   if ( pGotoList_->nGetNumGotoItems() == 0 ) {
      GuiApp::popupErrorMessage( "This command doesn't make sense with an empty list" );
      return;
   }

   if (wid == widSaveButton_ ) {
     saveNavigatorList();
     return;
   }

   int nCurIndex;

   int* pPositionList;
   int nNumberOfSelectedItems;
   if ( XmListGetSelectedPos( widList_, &pPositionList,
                              &nNumberOfSelectedItems ) ) {
      
      if ( nNumberOfSelectedItems == 0 ) {
         nCurIndex = navigatorNoSelection;
      }
      else {
         assert( nNumberOfSelectedItems == 1 );
         nCurIndex = pPositionList[0];
      }

      XtFree( (char*) pPositionList );
   }
   else 
      nCurIndex = navigatorNoSelection;


   if ( wid == widSpecialPurposeButton_ ) {

      gotoItem* pGotoItem;
      if ( nCurIndex == navigatorNoSelection )
         pGotoItem = NULL;
      else {
         // -1 since the Motif list is 1-based and the Rogue Wave list
         // is 0-based
         pGotoItem = (*pGotoList_)[ nCurIndex - 1];
      }

      pcbSpecialPurposeButton_( pGotoItem,
                                pClientDataForSpecialPurposeButton_ );
      return;
   }

   int nGotoIndex;  // where we want to go (may be different from currently
       // selected item if the user pushes next or prev

   if (wid == widGoButton_ || wid == widList_ ) {
      if ( ( wid == widGoButton_ ) && 
           ( nCurIndex == navigatorNoSelection ) ) {
         GuiApp::popupErrorMessage( "First click on an item before clicking on Go" );
         return;
      }

      nGotoIndex = nCurIndex;
   }
   else if (wid == widNextButton_ ) {
      // which one is "next"?
      if (nCurrentSelection_ == navigatorNoSelection ) {
         nGotoIndex = 1;  // go to first one
      }
      else if (nCurrentSelection_ < nGetMaxIndex()) {
         nGotoIndex = nCurrentSelection_ + 1;
      }
      else {
         nGotoIndex = navigatorNoSelection;
      }

   }
   else if (wid == widPrevButton_ ) {
      // which one is "prev"?
      if ((nCurrentSelection_ == navigatorNoSelection ) ||
          (nCurrentSelection_ == 1) ) {
         nGotoIndex = 1;  // go to first one
      }
      else {
         nGotoIndex = nCurrentSelection_ - 1;
      }

   }
   else
      assert(false);

   if (nGotoIndex != navigatorNoSelection) {

      // highlight the position we are going to


      int nTopIndex;
      int nVisibleItems;
   
      XtVaGetValues( widList_,
                     XmNtopItemPosition, &nTopIndex,
                     XmNvisibleItemCount, &nVisibleItems,
                     NULL );

      // motif list's start at 1
      int nIndexInMotifList = nGotoIndex;

      if ( nIndexInMotifList < nTopIndex )
         XmListSetPos( widList_, nIndexInMotifList );
      else if (nIndexInMotifList > nTopIndex + nVisibleItems - 1)
         XmListSetBottomPos( widList_, nIndexInMotifList );
   
      XmListSelectPos( widList_, nIndexInMotifList, True );


      // set the current selection member data

      // long winded debug version
      nCurrentSelection_ = nGotoIndex;
      // because nGotoIndex starts at 1 but gotoList starts at 0
      gotoItem* pGotoItem = (*pGotoList_)[nGotoIndex - 1];
      int nConsPos = pGotoItem->nGetStart();
      Contig* pContig = pGotoItem->pGetContig();

      // this can happen, for example, with hits against singletons
      if (!pContig ) return;


      // this fixes the following bug:  if you bring up a contig,
      // and then you bring it up again, and then you bring up a nav window,
      // and you click 'next', it will scroll the first one--not the
      // one you brought up the nav window from.  Now fixed (DG, 1/17/99
      // in Iceland!)

      ContigWin* pContigWin = NULL;

      if (pGotoItem->pGetLocFrag() ) {

         if ( pContigWin_ ) {
            pContigWin = pContigWin_;
            // the moveCursorToConsPos doesn't scroll the aligned reads
            // window--it just moves the cursor.  Thus we must first
            // scroll so this position is visible
            pContigWin->scrollToConsensusPosInCenter( nConsPos );

         }
         else
            pContigWin = ConsEd::pGetConsEd()->pScrollExistingContigWinOrMakeNewContigWin( pContig, 
                                                                                           nConsPos );

         pContigWin->moveCursorToFragPos( nConsPos, pGotoItem->pGetLocFrag() );
      }
      else {

         if ( pContigWin_ ) {
            pContigWin = pContigWin_;
            pContigWin->scrollToConsensusPosInCenterAndSetCursorOnConsensus( nConsPos );
         }
         else {
            pContigWin = ConsEd::pGetConsEd()->pScrollExistingContigWinOrMakeNewContigWinAndSetCursorOnConsensus( pContig, 
                         nConsPos );
         }
      }


      // raise the window
      pContigWin->raiseWindow();
      
      if ( consedParameters::pGetConsedParameters()->bNavigateAutomaticTracePopup_ ) {

         // check if this is on a read
         if ( pGotoItem->pGetLocFrag() ) {
            // if on a read, bring up the trace
            pContigWin->scrollExistingTracesOrPopupIfNecessary( 
                             pGotoItem->pGetLocFrag(),
                             nConsPos );

         }
      }

      if ( consedParameters::pGetConsedParameters()->bNavigateAutomaticAllTracesPopup_ ) {

         // check if this is on the consensus
         if ( ! (pGotoItem->pGetLocFrag() ) ) {
            // if on the consensus, bring up all traces
            pContigWin->showAllTracesByConsensusPosition( nConsPos );
         }
      }
   }
}




void guiMultiContigNavigator :: saveNavigatorList() {
  RWCString soDirMask = "*.*";
  RWCString soTryOutFileName = "list.txt";

   FileName soUserOutFileName =
     GuiApp::popupFileSelector("Save list to file", 
                               soDirMask,
                               soTryOutFileName);

   // if user cancelled or did not supply name, bail now
   if (soUserOutFileName.isNull()) { return; }

   bool bGoAhead = true;
   if (soUserOutFileName.bFileByThisNameExists()) {
      bGoAhead = 
        GuiApp::popupDecisionMessage("File %s exists.  Save anyway?",
                                     (const char*)soUserOutFileName);
   }
   if (! bGoAhead) return;
   
   try {
     saveNavigatorList2( soUserOutFileName );
   }
   catch (SysRequestFailed srf) {
      GuiApp::popupErrorMessage(srf.szGetDesc());
   }

}
  


void guiMultiContigNavigator :: saveNavigatorList2( const RWCString& soFilename ) {

   // open the output file
   ofstream ofsNavigatorListFile( soFilename, ios::out);
   if (! ofsNavigatorListFile) {
      // throw an exception with a detailed explanation
      ostringstream ost; 
      ost << "Unable to open file " << soFilename 
          << " for writing" << endl << ends;
      SysRequestFailed srf(ost.str().c_str());
      // what the hell, show 'em the errno
      srf.includeErrnoDescription();
      throw srf;
   }

   // how many gotoItems in the list?
   int nNumGotoItems = pGotoList_->nGetNumGotoItems();

   for (int n = 0; n < nNumGotoItems; n++) {
     ofsNavigatorListFile  << (*pGotoList_)[n]->soGetFullDesc() << endl;
   }
   
   ofsNavigatorListFile.close();
   
}



void guiMultiContigNavigator :: appendToMultiContigNavigator( 
                                             gotoItem* pGotoItemToAppend ) {

   
   pGotoList_->addToList( pGotoItemToAppend );

   XmString xms =
        // get char* from gotoItem* from gotoList*
        XmStringCreateSimple((char*)( pGotoItemToAppend->soGetFullDesc().data()));
   
   int nOneBasedIndex = pGotoList_->nGetNumGotoItems();

   XmListAddItem( widList_, xms, nOneBasedIndex );

}


                             
                             

void guiMultiContigNavigator :: appendToList ( gotoItem* pGotoItemToAppend ) {
   
   pGotoList_->addToList( pGotoItemToAppend );

}



void guiMultiContigNavigator :: displayList( const bool bSortByStartPosition ) {

   if ( bSortByStartPosition ) 
      pGotoList_->sortByPosition();

   XmString* pXmStrings;

   pXmStrings = (XmString*) XtMalloc( sizeof( XmString ) *
                                      pGotoList_->nGetNumGotoItems() );

   int nGotoItem;
   for( nGotoItem = 0;
        nGotoItem < pGotoList_->nGetNumGotoItems();
        ++nGotoItem ) {

      gotoItem* pGotoItem = pGotoList_->pGetGotoItem( nGotoItem );
      
      pXmStrings[ nGotoItem ] =
         XmStringCreateSimple( (char*) pGotoItem->soGetFullDesc().data() );

   }

   XtVaSetValues( widList_,
                  XmNitems, pXmStrings,
                  XmNitemCount, pGotoList_->nGetNumGotoItems(),
                  NULL );

   for( nGotoItem = 0; nGotoItem < pGotoList_->nGetNumGotoItems(); ++nGotoItem )
      XmStringFree( pXmStrings[ nGotoItem ] );
   
   XtFree( (char*) pXmStrings );

}


void guiMultiContigNavigator :: gotoNextOrPreviousItem( const bool bNextNotPrevious ) {

   Widget wid = ( bNextNotPrevious ? widNextButton_ : widPrevButton_ );

   guiMultiContigNavigatorXtButtonCb2( wid  );

}



guiMultiContigNavigator :: ~guiMultiContigNavigator() {
   if ( pContigWin_ ) {
      // allow the possibility that the same aligned reads window
      // has several different navigate windows up at once
      if ( pContigWin_->pGuiMultiContigNav_ == this )
         pContigWin_->pGuiMultiContigNav_ = NULL;
   }
   else if ( pAssemblyView_ ) {
      pAssemblyView_->pGuiNav_ = NULL;
   }
   else {
      ConsEd::pGetConsEd()->aGuiMultiContigNavigator_.remove( this );
   }

   // there is a memory leak here--the gotoList should be deallocated

   unmanage();
   XtDestroyWidget( widPopupShell_ );

}


void guiMultiContigNavigator ::  raiseWindow() {

   XtMapWidget( widPopupShell_ );
   
   XRaiseWindow(
                XtDisplay( widPopupShell_ ),
                XtWindow( widPopupShell_ )
                );
}



void guiMultiContigNavigator :: scrollDownToBottom() {

   int nVisibleItemCount;

   XtVaGetValues( widList_,
                  XmNvisibleItemCount, &nVisibleItemCount,
                  NULL );

   if ( pGotoList_->nGetNumGotoItems() > nVisibleItemCount ) {

      XtVaSetValues( widList_,
                  XmNtopItemPosition, 
                     pGotoList_->nGetNumGotoItems() - nVisibleItemCount + 1,
                  NULL );
   }
}