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 1fd72c4..b804681 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -186,16 +186,16 @@ public final class MainFrameApplet extends MainFrame {
                         .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
                 MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
                         .getTreeFontSet() ) );
-                MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
-                                                                     _show_scale_cbmi,
-                                                                     _show_branch_length_values_cbmi,
-                                                                     _non_lined_up_cladograms_rbmi,
-                                                                     _uniform_cladograms_rbmi,
-                                                                     _ext_node_dependent_cladogram_rbmi,
-                                                                     _label_direction_cbmi );
                 MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
                 MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
                 MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
+                try {
+                    getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
+                    getMainPanel().getControlPanel().setVisibilityOfX();
+                }
+                catch ( final Exception ignore ) {
+                    // do nothing, not important.
+                }
             }
         } );
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
@@ -212,14 +212,14 @@ public final class MainFrameApplet extends MainFrame {
         _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_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 ) );
         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
@@ -273,13 +273,14 @@ public final class MainFrameApplet extends MainFrame {
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-        customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
         customizeCheckBoxMenuItem( _label_direction_cbmi,
                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
+        customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -289,8 +290,13 @@ 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" ) );
@@ -304,9 +310,4 @@ public final class MainFrameApplet extends MainFrame {
     JApplet getApplet() {
         return _applet;
     }
-
-    @Override
-    void readPhylogeniesFromURL() {
-        throw new NoSuchMethodError( "not implemented" );
-    }
 }