+ private void setupDisplayCheckboxes() {
+ if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
+ addCheckbox( Configuration.display_as_phylogram,
+ _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
+ setCheckbox( Configuration.display_as_phylogram,
+ _configuration.doCheckOption( Configuration.display_as_phylogram ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
+ addCheckbox( Configuration.dynamically_hide_data,
+ _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
+ setCheckbox( Configuration.dynamically_hide_data,
+ _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
+ addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
+ setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
+ addCheckbox( Configuration.display_internal_data,
+ _configuration.getDisplayTitle( Configuration.display_internal_data ) );
+ setCheckbox( Configuration.display_internal_data,
+ _configuration.doCheckOption( Configuration.display_internal_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
+ addCheckbox( Configuration.color_according_to_sequence,
+ _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
+ setCheckbox( Configuration.color_according_to_sequence,
+ _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
+ addCheckbox( Configuration.color_according_to_species,
+ _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
+ setCheckbox( Configuration.color_according_to_species,
+ _configuration.doCheckOption( Configuration.color_according_to_species ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
+ addCheckbox( Configuration.color_according_to_annotation,
+ _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
+ setCheckbox( Configuration.color_according_to_annotation,
+ _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
+ addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
+ setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
+ addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
+ setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
+ }
+ final JLabel label = new JLabel( "Display Data:" );
+ label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ add( label );
+ if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
+ addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
+ setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
+ addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
+ setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
+ setCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
+ setCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
+ addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
+ setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
+ addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
+ setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
+ addCheckbox( Configuration.show_seq_symbols,
+ _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
+ setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
+ addCheckbox( Configuration.show_sequence_acc,
+ _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
+ setCheckbox( Configuration.show_sequence_acc,
+ _configuration.doCheckOption( Configuration.show_sequence_acc ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
+ addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
+ setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
+ addCheckbox( Configuration.write_confidence_values,
+ _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
+ setCheckbox( Configuration.write_confidence_values,
+ _configuration.doCheckOption( Configuration.write_confidence_values ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
+ addCheckbox( Configuration.write_branch_length_values,
+ _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
+ setCheckbox( Configuration.write_branch_length_values,
+ _configuration.doCheckOption( Configuration.write_branch_length_values ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
+ addCheckbox( Configuration.show_binary_characters,
+ _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
+ setCheckbox( Configuration.show_binary_characters,
+ _configuration.doCheckOption( Configuration.show_binary_characters ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
+ addCheckbox( Configuration.show_binary_character_counts,
+ _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
+ setCheckbox( Configuration.show_binary_character_counts,
+ _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
+ addCheckbox( Configuration.show_domain_architectures,
+ _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
+ setCheckbox( Configuration.show_domain_architectures,
+ _configuration.doCheckOption( Configuration.show_domain_architectures ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
+ addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
+ setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
+ addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
+ setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
+ addCheckbox( Configuration.show_vector_data,
+ _configuration.getDisplayTitle( Configuration.show_vector_data ) );
+ setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
+ addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
+ setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
+ addCheckbox( Configuration.show_taxonomy_images,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
+ setCheckbox( Configuration.show_taxonomy_images,
+ _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
+ }