cleanup

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0f7fd20..6248f6d 100644 (file)
--- 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;
@@ -209,6 +208,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
     JCheckBoxMenuItem           _replace_underscores_cbmi;
+    JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;
     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
     // _  search
@@ -407,9 +407,6 @@ 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 +421,18 @@ 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 +1280,6 @@ 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 );
         }
@@ -1347,6 +1345,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
                 && _replace_underscores_cbmi.isSelected() );
+        options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+                && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
@@ -1427,7 +1427,7 @@ 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,