X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=3738cf41ed513a3b53ee063209b93bc40910a865;hb=28cf1afacf61a15e72411b1e58c3694f78d6d0dd;hp=7ea1610428ea3667ab103173d76bb2d9446b7790;hpb=af5e25d369f3240ce41018957383044c12126d98;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 7ea1610..3738cf4 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -115,6 +115,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JCheckBoxMenuItem           _search_case_senstive_cbmi;
     private JCheckBoxMenuItem           _search_whole_words_only_cbmi;
     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
+    private JCheckBoxMenuItem           _search_with_regex_cbmi;
     private JCheckBoxMenuItem           _show_overview_cbmi;
     private JMenuItem                   _choose_minimal_confidence_mi;
     private JMenuItem                   _collapse_species_specific_subtrees;
@@ -122,6 +123,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private ButtonGroup                 _radio_group_1;
     private JCheckBoxMenuItem           _show_default_node_shapes_internal_cbmi;
     private JCheckBoxMenuItem           _show_default_node_shapes_external_cbmi;
+    private JCheckBoxMenuItem           _show_default_node_shapes_for_marked_cbmi;
     private JMenuItem                   _cycle_node_shape_mi;
     private JMenuItem                   _cycle_node_fill_mi;
     private JMenuItem                   _choose_node_size_mi;
@@ -250,6 +252,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             getMainPanel().getControlPanel().search1();
         }
         else if ( o == _search_whole_words_only_cbmi ) {
+            if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
+                _search_with_regex_cbmi.setSelected( false );
+            }
             updateOptions( getOptions() );
             getMainPanel().getControlPanel().search0();
             getMainPanel().getControlPanel().search1();
@@ -259,6 +264,17 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             getMainPanel().getControlPanel().search0();
             getMainPanel().getControlPanel().search1();
         }
+        else if ( o == _search_with_regex_cbmi ) {
+            if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+                _search_whole_words_only_cbmi.setSelected( false );
+            }
+            if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+                _search_case_senstive_cbmi.setSelected( true );
+            }
+            updateOptions( getOptions() );
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
+        }
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -751,13 +767,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
-        /////
         _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_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 ) );
+        _options_jmenu
+                .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 ) );
@@ -782,13 +799,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
-        /////
         _options_jmenu.addSeparator();
         _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
                                                                 getConfiguration() ) );
         _options_jmenu
                 .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 );
@@ -807,6 +825,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
                 .isShowDefaultNodeShapesInternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
+                .isShowDefaultNodeShapesForMarkedNodes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
@@ -820,6 +840,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
+        customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
@@ -1309,6 +1330,8 @@ public class ArchaeopteryxE extends JApplet 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.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+                && _show_default_node_shapes_for_marked_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }
@@ -1336,6 +1359,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 && _show_confidence_stddev_cbmi.isSelected() );
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
+        options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
                 && _inverse_search_result_cbmi.isSelected() );
         if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {