X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplet.java;h=1fd72c463bd0c4e2ee20e7410069461efead0314;hb=7359853f540f8d2704930c90e0ea9b6969bde51b;hp=11bbba5f3984ad015bb911c6f2b60fd7eb361f98;hpb=733f051a048f64b6850314a08880f1f77a633db8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 11bbba5..1fd72c4 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -208,34 +208,38 @@ 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_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
         _options_jmenu
-                .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+                .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( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+                .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( _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( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
-        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
-        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
-        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
-        _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
-        _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
+                .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+        _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 ) );
+        _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
+        _label_direction_cbmi.setToolTipText( MainFrame.LABEL_DIRECTION_TIP );
         _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( MainFrame.SCREEN_ANTIALIAS_LABEL ) );
         _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( MainFrame.BG_GRAD_LABEL ) );
-        if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
-            _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
-        }
+        _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+        _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+        _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
         _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
         _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() ) );
@@ -251,14 +255,15 @@ 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 );
+        customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
         customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
         customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
         customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
         customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+        customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
         customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );