_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() );
_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 ) );
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 );
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();
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 );
}
|| 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 );
}
@Override
public String getDescription() {
- return "NHX files (*.nhx)";
+ return "NHX files (*.nhx) [deprecated]";
}
}