X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=fc6bb326652a78c435dc656613f1697c5a46daae;hb=7359853f540f8d2704930c90e0ea9b6969bde51b;hp=0f7fd20b5774673287f93d3921516b3aacedbaa4;hpb=b4d39d202d7162aed8a41f2e1c42ac81f91c9341;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0f7fd20..fc6bb32 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -192,7 +192,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _cycle_node_shape_mi;
     JMenuItem                   _cycle_node_fill_mi;
     JMenuItem                   _choose_node_size_mi;
-    JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
     // _  print
     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
@@ -407,9 +406,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_default_node_shapes_external_cbmi ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
-            updateOptions( getOptions() );
-        }
         else if ( o == _non_lined_up_cladograms_rbmi ) {
             updateOptions( getOptions() );
             showWhole();
@@ -424,15 +420,18 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
         else if ( o == _search_case_senstive_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _search_whole_words_only_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _inverse_search_result_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
@@ -1280,8 +1279,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
                 && _show_default_node_shapes_external_cbmi.isSelected() );
-        options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
-                && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }
@@ -1427,7 +1424,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     private void annotateSequences() {
         if ( getCurrentTreePanel() != null ) {
-            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
             if ( ( nodes == null ) || nodes.isEmpty() ) {
                 JOptionPane
                         .showMessageDialog( this,