added a close button

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 8ede385..b940f35 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -121,7 +121,7 @@ public final class MainFrameApplication extends MainFrame {
     private ButtonGroup                  _radio_group_1;\r
     private ButtonGroup                  _radio_group_2;\r
     // Others:\r
-    double                               _min_not_collapse               = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+    double                               _min_not_collapse               = AptxConstants.MIN_NOT_COLLAPSE_DEFAULT;\r
     double                               _min_not_collapse_bl            = 0.001;\r
     // Phylogeny Inference menu\r
     private JMenu                        _inference_menu;\r
@@ -197,7 +197,7 @@ public final class MainFrameApplication extends MainFrame {
         }\r
         try {\r
             boolean synth_exception = false;\r
-            if ( Constants.__SYNTH_LF ) {\r
+            if ( AptxConstants.__SYNTH_LF ) {\r
                 try {\r
                     final SynthLookAndFeel synth = new SynthLookAndFeel();\r
                     synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),\r
@@ -206,12 +206,12 @@ public final class MainFrameApplication extends MainFrame {
                 }\r
                 catch ( final Exception ex ) {\r
                     synth_exception = true;\r
-                    ForesterUtil.printWarningMessage( Constants.PRG_NAME,\r
+                    ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME,\r
                                                       "could not create synth look and feel: "\r
                                                               + ex.getLocalizedMessage() );\r
                 }\r
             }\r
-            if ( !Constants.__SYNTH_LF || synth_exception ) {\r
+            if ( !AptxConstants.__SYNTH_LF || synth_exception ) {\r
                 if ( _configuration.isUseNativeUI() ) {\r
                     UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );\r
                 }\r
@@ -242,7 +242,7 @@ public final class MainFrameApplication extends MainFrame {
         setInferenceManager( InferenceManager.createInstance( _configuration ) );\r
         setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );\r
         // set title\r
-        setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );\r
+        setTitle( AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + " (" + AptxConstants.PRG_DATE + ")" );\r
         _mainpanel = new MainPanel( _configuration, this );\r
         // The file dialogs\r
         _open_filechooser = new JFileChooser();\r
@@ -296,7 +296,7 @@ public final class MainFrameApplication extends MainFrame {
             _jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
         }\r
         buildFileMenu();\r
-        if ( Constants.__ALLOW_PHYLOGENETIC_INFERENCE ) {\r
+        if ( AptxConstants.__ALLOW_PHYLOGENETIC_INFERENCE ) {\r
             buildPhylogeneticInferenceMenu();\r
         }\r
         buildAnalysisMenu();\r
@@ -1844,6 +1844,7 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
         _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
         _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
+        _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) ); \r
         _options_jmenu.addSeparator();\r
         _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
                                                       getConfiguration() ) );\r
@@ -1858,7 +1859,7 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
         _options_jmenu.addSeparator();\r
-        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );\r
         _options_jmenu\r
         .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
@@ -1882,7 +1883,7 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
         _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
-        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );\r
         _options_jmenu\r
         .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
         _use_brackets_for_conf_in_nh_export_cbmi\r
@@ -1941,6 +1942,7 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
+        customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() ); \r
         customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r