in progress (special coloring is still true)

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplet.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index b804681..43fdc2e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -208,18 +208,19 @@ public final class MainFrameApplet extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
-        ////////////
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+        _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
         }
-        _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu
@@ -239,7 +240,6 @@ public final class MainFrameApplet extends MainFrame {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
-        //////
         _options_jmenu.addSeparator();
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
                                                                 getConfiguration() ) );
@@ -255,6 +255,8 @@ public final class MainFrameApplet extends MainFrame {
                 .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
                 .isShowDefaultNodeShapesExternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+                .isShowDefaultNodeShapesForMarkedNodes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );