- void buildOptionsMenu() {
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );
- _options_jmenu.addChangeListener( new ChangeListener() {
-
- @Override
- public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
- MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
- setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),
- _show_scale_cbmi,
- _show_branch_length_values_cbmi,
- _non_lined_up_cladograms_rbmi,
- _uniform_cladograms_rbmi,
- _ext_node_dependent_cladogram_rbmi,
- _label_direction_cbmi );
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
- MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
- }
- } );
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
- _options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
- _radio_group_1 = new ButtonGroup();
- _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
- _radio_group_1.add( _uniform_cladograms_rbmi );
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
- _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
- _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( _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 ) );
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
- _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
- _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
- _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
- _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
- _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
- }
- _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );
- _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );
- _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
- getConfiguration() ) );
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
- _options_jmenu
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
- _options_jmenu
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
- _options_jmenu
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
- _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
- _options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
- _options_jmenu
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
- //
- _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
- _options_jmenu
- .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
- _extract_taxonomy_pfam_rbmi
- .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
- _options_jmenu
- .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
- _extract_taxonomy_yes_rbmi
- .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
- _radio_group_2 = new ButtonGroup();
- _radio_group_2.add( _extract_taxonomy_no_rbmi );
- _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
- _radio_group_2.add( _extract_taxonomy_yes_rbmi );
- //
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
- _options_jmenu
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
- _use_brackets_for_conf_in_nh_export_cbmi
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
- _options_jmenu
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
- customizeJMenuItem( _choose_font_mi );
- customizeJMenuItem( _choose_minimal_confidence_mi );
- customizeJMenuItem( _switch_colors_mi );
- customizeJMenuItem( _print_size_mi );
- customizeJMenuItem( _choose_pdf_width_mi );
- customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
- customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
- customizeJMenuItem( _cycle_node_shape_mi );
- customizeJMenuItem( _cycle_node_fill_mi );
- customizeJMenuItem( _choose_node_size_mi );
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
- customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
- customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
- customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
- customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
- customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
- customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
- customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
- customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
- customizeCheckBoxMenuItem( _label_direction_cbmi,
- getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
- customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
- customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
- .isInternalNumberAreConfidenceForNhParsing() );
- customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
- customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
- customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
- customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
- customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
- customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
- customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
- .isGraphicsExportUsingActualSize() );
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
- _jmenubar.add( _options_jmenu );