inprogress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index a855d90..286bf47 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -97,6 +97,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _aptx_ref_item;
     private JMenuItem                   _remove_branch_color_item;
     private JCheckBoxMenuItem           _show_domain_labels;
+    private JCheckBoxMenuItem           _show_annotation_ref_source;
     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
     private JCheckBoxMenuItem           _abbreviate_scientific_names;
     private JCheckBoxMenuItem           _screen_antialias_cbmi;
@@ -262,6 +263,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _label_direction_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _abbreviate_scientific_names ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _show_overview_cbmi ) {
             updateOptions( getOptions() );
             if ( getCurrentTreePanel() != null ) {
@@ -742,6 +746,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         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( _show_default_node_shapes_external_cbmi, getOptions()
                 .isShowDefaultNodeShapesExternal() );
@@ -812,7 +817,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu
+                .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
@@ -1276,6 +1282,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
                 && _background_gradient_cbmi.isSelected() );
         options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+        options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+                && _show_annotation_ref_source.isSelected() );
         options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
                 && _abbreviate_scientific_names.isSelected() );
         options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )