in progress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 125471d..e0d7990 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -901,13 +901,14 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
         _radio_group_1.add( _uniform_cladograms_rbmi );\r
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
-        ///////\r
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
         _options_jmenu\r
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
         _options_jmenu\r
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+        _options_jmenu\r
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
@@ -930,7 +931,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
-        ///////\r
         _options_jmenu.addSeparator();\r
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
         _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
@@ -956,7 +956,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
         _options_jmenu\r
                 .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
-        //\r
         _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
         _options_jmenu\r
                 .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
@@ -975,7 +974,6 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
-        // \r
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
         _options_jmenu\r
                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
@@ -993,6 +991,8 @@ public final class MainFrameApplication extends MainFrame {
                 .isShowDefaultNodeShapesExternal() );\r
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
                 .isShowDefaultNodeShapesInternal() );\r
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+                .isShowDefaultNodeShapesForMarkedNodes() );\r
         customizeJMenuItem( _cycle_node_shape_mi );\r
         customizeJMenuItem( _cycle_node_fill_mi );\r
         customizeJMenuItem( _choose_node_size_mi );\r