inprogress

[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 ca14a87..b50cbf2 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -302,7 +302,6 @@ public final class MainFrameApplication extends MainFrame {
         _save_filechooser.setCurrentDirectory( new File( "." ) );
         _save_filechooser.setMultiSelectionEnabled( false );
         _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );
-        _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );
         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );
         _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );
         _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
@@ -963,7 +962,10 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu
                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
-        _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
         _options_jmenu
                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
@@ -1034,7 +1036,10 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _print_size_mi );
         customizeJMenuItem( _choose_pdf_width_mi );
         customizeJMenuItem( _overview_placment_mi );
-        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+                .isShowDefaultNodeShapesExternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+                .isShowDefaultNodeShapesInternal() );
         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
@@ -2474,18 +2479,6 @@ public final class MainFrameApplication extends MainFrame {
         return exception;
     }
 
-    private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) {
-        try {
-            final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toNewHampshireX( t, file );
-        }
-        catch ( final Exception e ) {
-            exception = true;
-            exceptionOccuredDuringSaveAs( e );
-        }
-        return exception;
-    }
-
     private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
@@ -2560,9 +2553,6 @@ public final class MainFrameApplication extends MainFrame {
             if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {
                 exception = writeAsNewHampshire( t, exception, file );
             }
-            else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) {
-                exception = writeAsNHX( t, exception, file );
-            }
             else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {
                 exception = writeAsPhyloXml( t, exception, file );
             }
@@ -2576,9 +2566,6 @@ public final class MainFrameApplication extends MainFrame {
                         || file_name.endsWith( ".tree" ) ) {
                     exception = writeAsNewHampshire( t, exception, file );
                 }
-                else if ( file_name.endsWith( ".nhx" ) ) {
-                    exception = writeAsNHX( t, exception, file );
-                }
                 else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {
                     exception = writeAsNexus( t, exception, file );
                 }
@@ -2816,7 +2803,7 @@ class NHXFilter extends FileFilter {
 
     @Override
     public String getDescription() {
-        return "NHX files (*.nhx)";
+        return "NHX files (*.nhx) [deprecated]";
     }
 }