- void endClickToOptions() {
- _click_to_combobox.addActionListener( this );
- }
-
- /**
- * Indicates what action should be execute when a node is clicked
- *
- * @return the click-on action
- */
- NodeClickAction getActionWhenNodeClicked() {
- return _action_when_node_clicked;
- }
-
- Map<Integer, String> getAllClickToItems() {
- return _all_click_to_names;
- }
-
- Map<String, Color> getAnnotationColors() {
- return _annotation_colors;
- }
-
- Configuration getConfiguration() {
- return _configuration;
- }
-
- TreePanel getCurrentTreePanel() {
- return getMainPanel().getCurrentTreePanel();
- }
-
- MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- Options getOptions() {
- return getMainPanel().getOptions();
- }
-
- JLabel getSearchFoundCountsLabel0() {
- return _search_found_label_0;
- }
-
- JLabel getSearchFoundCountsLabel1() {
- return _search_found_label_1;
- }
-
- JButton getSearchResetButton0() {
- return _search_reset_button_0;
- }
-
- JButton getSearchResetButton1() {
- return _search_reset_button_1;
- }
-
- JTextField getSearchTextField0() {
- return _search_tf_0;
- }
-
- JTextField getSearchTextField1() {
- return _search_tf_1;
- }
-
- List<String> getSingleClickToNames() {
- return _click_to_names;
- }
-
- Map<String, Color> getSpeciesColors() {
- return _species_colors;
- }
-
- Map<String, Color> getSequenceColors() {
- return _sequence_colors;
- }
-
- boolean isAntialiasScreenText() {
- return true;
- }
-
- boolean isColorAccordingToAnnotation() {
- return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
- }
-
- boolean isColorAccordingToTaxonomy() {
- return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
- }
-
- boolean isColorAccordingToSequence() {
- return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
- }
-
- boolean isUseVisualStyles() {
- return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
- }
-
- boolean isDrawPhylogram() {
- return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
- }
-
- boolean isDynamicallyHideData() {
- return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
- }
-
- boolean isEvents() {
- return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
- }
-
- boolean isNodeDescPopup() {
- return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
- }
-
- boolean isShowAnnotation() {
- return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
- }
-
- boolean isShowBinaryCharacterCounts() {
- return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
- }
-
- boolean isShowBinaryCharacters() {
- return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
- }
-
- boolean isShowConfidenceValues() {
- return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
- }
-
- boolean isWriteBranchLengthValues() {
- return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
- }
-
- boolean isShowDomainArchitectures() {
- return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
- }
-
- public boolean isShowMolSequences() {
- return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
- }
-
- boolean isShowGeneNames() {
- return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
- }
-
- boolean isShowInternalData() {
- return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
- }
-
- boolean isShowNodeNames() {
- return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
- }
-
- boolean isShowSeqNames() {
- return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
- }
-
- boolean isShowSeqSymbols() {
- return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
- }
-
- boolean isShowSequenceAcc() {
- return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
- }
-
- boolean isShowSequenceRelationConfidence() {
- return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
- }
-
- boolean isShowSequenceRelations() {
- return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
- }
-
- boolean isShowTaxonomyCode() {
- return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
- }
-
- boolean isShowTaxonomyCommonNames() {
- return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
- }
-
- boolean isShowTaxonomyScientificNames() {
- return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
- }
-
- boolean isWidthBranches() {
- return ( ( _width_branches != null ) && _width_branches.isSelected() );
- }
-
- void phylogenyAdded( final Configuration configuration ) {
- getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
- }
-
- void phylogenyRemoved( final int index ) {
- getIsDrawPhylogramList().remove( index );
- }
-
- void search0() {
- final MainPanel main_panel = getMainPanel();
- final Phylogeny tree = main_panel.getCurrentPhylogeny();
- if ( ( tree == null ) || tree.isEmpty() ) {
- return;
+ 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 ) );