Fix some menu items being inactive in the BDV views.

The menu builder must be called apparently AFTER the corresponding
actions have been installed. Lest these actions are inactive when
called from the menu (but this works with a shortcut).

This requires some gymnastic, because the coloring requires the
menu handles to be built before. So we declare those early in the
initialization process. And to keep the future menu
order, we build an empty menu but already with all su-bmenus in
order.
Then at the end of the initialization process we flesh out all the
menu items.

Author: tinevez

src/main/java/org/mastodon/mamut/MamutViewBdv.java

@@ -155,43 +155,38 @@ public MamutViewBdv( final MamutAppModel appModel, final Map< String, Object > g
 		MastodonFrameViewActions.install( viewActions, this );
 		BigDataViewerActionsMamut.install( viewActions, bdv );
 
-		final ViewMenu menu = new ViewMenu( this );
-		final ActionMap actionMap = frame.getKeybindings().getConcatenatedActionMap();
-
+		
+		/*
+		 * We have to build the coloring menu handles now. But the other actions
+		 * need to be included in the menus later, after they have been
+		 * installed (otherwise they won't be active). To keep the future menu
+		 * order, we build an empty menu but already with all su-bmenus in
+		 * order.
+		 */
 		final JMenuHandle menuHandle = new JMenuHandle();
 		final JMenuHandle tagSetMenuHandle = new JMenuHandle();
 		final JMenuHandle colorbarMenuHandle = new JMenuHandle();
-		MainWindow.addMenus( menu, actionMap );
+		final ViewMenu menu = new ViewMenu( this );
+		final ActionMap actionMap = frame.getKeybindings().getConcatenatedActionMap();
 		MamutMenuBuilder.build( menu, actionMap,
-				fileMenu(
-						separator(),
-						item( BigDataViewerActions.LOAD_SETTINGS ),
-						item( BigDataViewerActions.SAVE_SETTINGS ),
-						separator(),
-						item( RecordMovieDialog.RECORD_MOVIE_DIALOG ),
-						item( RecordMaxProjectionMovieDialog.RECORD_MIP_MOVIE_DIALOG ) ),
+				fileMenu(),
 				viewMenu(
 						colorMenu( menuHandle ),
-						colorbarMenu( colorbarMenuHandle ),
-						separator(),
-						item( MastodonFrameViewActions.TOGGLE_SETTINGS_PANEL ) ),
-				editMenu(
-						item( UndoActions.UNDO ),
-						item( UndoActions.REDO ),
-						separator(),
-						item( SelectionActions.DELETE_SELECTION ),
-						item( SelectionActions.SELECT_WHOLE_TRACK ),
-						item( SelectionActions.SELECT_TRACK_DOWNWARD ),
-						item( SelectionActions.SELECT_TRACK_UPWARD ),
-						separator(),
-						tagSetMenu( tagSetMenuHandle ) ),
-				ViewMenuBuilder.menu( "Settings",
-						item( BigDataViewerActions.BRIGHTNESS_SETTINGS ),
-						item( BigDataViewerActions.VISIBILITY_AND_GROUPING ) ) );
-		appModel.getPlugins().addMenus( menu );
+						colorbarMenu( colorbarMenuHandle ) ),
+				editMenu(),
+				ViewMenuBuilder.menu( "Settings" ) );
 
+		// The view panel.
 		viewer = bdv.getViewer();
 
+		// we need the coloring now.
+		final GraphColorGeneratorAdapter< Spot, Link, OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > coloring =
+				new GraphColorGeneratorAdapter<>( viewGraph.getVertexMap(), viewGraph.getEdgeMap() );
+		coloringModel = registerColoring( coloring, menuHandle,
+				() -> viewer.getDisplay().repaint() );
+		colorBarOverlay = new ColorBarOverlay( coloringModel, () -> viewer.getBackground() );
+		registerColorbarOverlay( colorBarOverlay, colorbarMenuHandle, () -> viewer.getDisplay().repaint() );
+
 		// Restore BDV state.
 		final Element stateEl = ( Element ) guiState.get( BDV_STATE_KEY );
 		if ( null != stateEl )
@@ -204,9 +199,6 @@ public MamutViewBdv( final MamutAppModel appModel, final Map< String, Object > g
 		else
 			viewer.state().setViewerTransform( tLoaded );
 
-		final GraphColorGeneratorAdapter< Spot, Link, OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > coloring =
-				new GraphColorGeneratorAdapter<>( viewGraph.getVertexMap(), viewGraph.getEdgeMap() );
-
 		final OverlayGraphRenderer< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > tracksOverlay = createRenderer(
 				viewGraph,
 				highlightModel,
@@ -221,20 +213,6 @@ public MamutViewBdv( final MamutAppModel appModel, final Map< String, Object > g
 		final Model model = appModel.getModel();
 		final ModelGraph modelGraph = model.getGraph();
 
-		coloringModel = registerColoring( coloring, menuHandle,
-				() -> viewer.getDisplay().repaint() );
-		colorBarOverlay = new ColorBarOverlay( coloringModel, () -> viewer.getBackground() );
-		registerColorbarOverlay( colorBarOverlay, colorbarMenuHandle, () -> viewer.getDisplay().repaint() );
-
-		registerTagSetMenu( tagSetMenuHandle,
-				() -> viewer.getDisplay().repaint() );
-
-		// Restore coloring.
-		restoreColoring( coloringModel, guiState );
-
-		// Restore colorbar state.
-		restoreColorbarState( colorBarOverlay, guiState );
-		viewer.getDisplay().overlays().add( colorBarOverlay );
 
 		highlightModel.listeners().add( () -> viewer.getDisplay().repaint() );
 		focusModel.listeners().add( () -> viewer.getDisplay().repaint() );
@@ -305,8 +283,43 @@ public MamutViewBdv( final MamutAppModel appModel, final Map< String, Object > g
 
 		frame.setVisible( true );
 
-//		if ( !bdv.tryLoadSettings( bdvFile ) ) // TODO
-//			InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() );
+		MainWindow.addMenus( menu, actionMap );
+		MamutMenuBuilder.build( menu, actionMap,
+				fileMenu(
+						separator(),
+						item( BigDataViewerActions.LOAD_SETTINGS ),
+						item( BigDataViewerActions.SAVE_SETTINGS ),
+						separator(),
+						item( RecordMovieDialog.RECORD_MOVIE_DIALOG ),
+						item( RecordMaxProjectionMovieDialog.RECORD_MIP_MOVIE_DIALOG ) ),
+				viewMenu(
+						separator(),
+						item( MastodonFrameViewActions.TOGGLE_SETTINGS_PANEL ) ),
+				editMenu(
+						item( UndoActions.UNDO ),
+						item( UndoActions.REDO ),
+						separator(),
+						item( SelectionActions.DELETE_SELECTION ),
+						item( SelectionActions.SELECT_WHOLE_TRACK ),
+						item( SelectionActions.SELECT_TRACK_DOWNWARD ),
+						item( SelectionActions.SELECT_TRACK_UPWARD ),
+						separator(),
+						tagSetMenu( tagSetMenuHandle ) ),
+				ViewMenuBuilder.menu( "Settings",
+						item( BigDataViewerActions.BRIGHTNESS_SETTINGS ),
+						item( BigDataViewerActions.VISIBILITY_AND_GROUPING ) ) );
+		appModel.getPlugins().addMenus( menu );
+
+		registerTagSetMenu( tagSetMenuHandle,
+				() -> viewer.getDisplay().repaint() );
+
+		// Restore coloring.
+		restoreColoring( coloringModel, guiState );
+
+		// Restore colorbar state.
+		restoreColorbarState( colorBarOverlay, guiState );
+		viewer.getDisplay().overlays().add( colorBarOverlay );
+
 	}
 
 	protected OverlayGraphRenderer< OverlayVertexWrapper< Spot, Link >, OverlayEdgeWrapper< Spot, Link > > createRenderer(