in progress

[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 a5cd07d..22332cd 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -219,14 +219,15 @@ public final class MainFrameApplet extends MainFrame {
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
         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( _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
                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
-                .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu
                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
@@ -257,7 +258,6 @@ public final class MainFrameApplet extends MainFrame {
                 .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
                 .isShowDefaultNodeShapesExternal() );
-        customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
@@ -292,8 +292,13 @@ public final class MainFrameApplet extends MainFrame {
         customizeJMenuItem( _confcolor_item );
         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
         customizeJMenuItem( _taxcolor_item );
-        _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
-        _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
+        _tools_menu.addSeparator();
+        _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+        _remove_visual_styles_item
+                .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+        customizeJMenuItem( _remove_visual_styles_item );
+        _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+        _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
         customizeJMenuItem( _remove_branch_color_item );
         _tools_menu.addSeparator();
         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
@@ -307,9 +312,4 @@ public final class MainFrameApplet extends MainFrame {
     JApplet getApplet() {
         return _applet;
     }
-
-    @Override
-    void readPhylogeniesFromURL() {
-        throw new NoSuchMethodError( "not implemented" );
-    }
 }