X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=d517e42c67e462b19ec265c71bc8e5f53c91d803;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=36afa089bfcfa48e9388b0218f2f681bf24a8f1b;hpb=b48d82f75a2ff2f4e181092080371b8ab1abd618;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 36afa08..d517e42 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -229,10 +229,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
         }
         else if ( o == _cycle_node_fill_mi ) {
-            MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+            MainFrame.cycleNodeFill( getOptions() );
         }
         else if ( o == _cycle_node_shape_mi ) {
-            MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+            MainFrame.cycleNodeShape( getOptions() );
         }
         else if ( o == _non_lined_up_cladograms_rbmi ) {
             updateOptions( getOptions() );
@@ -392,7 +392,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
      * has been selected by the user by clicking the "Return ..."
      * menu item. This method is expected to be called from Javascript or
      * something like it.
-     * 
+     *
      * @return current external node data as String
      */
     public String getCurrentExternalNodesDataBuffer() {
@@ -409,7 +409,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     /**
      * This method returns the current phylogeny as a string in the chosen format
-     * 
+     *
      * @param format must be NH, NHX, NEXUS or PHYLOXML
      * @return the phylogeny string
      * @author Herve Menager
@@ -436,10 +436,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     }
 
     /**
-     * This method returns a view of the current phylogeny in a chosen 
+     * This method returns a view of the current phylogeny in a chosen
      * graphics format, base64-encoded in a string so that in can be used
      * from javascript.
-     * 
+     *
      * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp)
      * @return the phylogeny string
      * @author Herve Menager
@@ -609,10 +609,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 @Override
                 public void componentResized( final ComponentEvent e ) {
                     if ( getMainPanel().getCurrentTreePanel() != null ) {
-                        getMainPanel().getCurrentTreePanel()
-                                .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(),
-                                                            getMainPanel().getCurrentTreePanel().getHeight(),
-                                                            getOptions().isAllowFontSizeChange() );
+                        getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
+                                                                                        .getCurrentTreePanel()
+                                                                                        .getWidth(),
+                                                                                        getMainPanel()
+                                                                                        .getCurrentTreePanel()
+                                                                                        .getHeight() );
                     }
                 }
             } );
@@ -774,7 +776,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
         _options_jmenu
-                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+                .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
         _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
             _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
@@ -806,6 +808,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
         _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
+        _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
         _options_jmenu
                 .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
         customizeJMenuItem( _choose_font_mi );