- boolean displaySequenceRelations() {
- return _display_sequence_relations;
- }
-
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
- }
-
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- /**
- * Will attempt to use the phylogeny to determine whether to check
- * this or not (e.g. phylogram)
- *
- */
- boolean doGuessCheckOption( final int which ) {
- return display_options[ which ][ 2 ].equals( "?" );
- }
-
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- return _annotation_colors;
- }
-
- int getBaseFontSize() {
- return _base_font_size;
- }
-
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
- }
-
- int getClickToOptionsCount() {
- return clickto_options.length;
- }
-
- String getClickToTitle( final int which ) {
- return clickto_options[ which ][ 0 ];
- }
-
- int getDefaultDisplayClicktoOption() {
- return default_clickto;
- }
-
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
- }
-
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
- }
-
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
- }
-
- int getGraphicsExportX() {
- return _graphics_export_x;
- }
-
- int getGraphicsExportY() {
- return _graphics_export_y;
- }
-
- Color getGuiBackgroundColor() {
- return _gui_background_color;
- }
-
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
- }
-
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
- }
-
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
- }
-
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
- }
-
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
- }
-
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
- }
-
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
- }
-
- int getMaxBaseFontSize() {
- return _max_base_font_size;
- }
-
- int getMinBaseFontSize() {
- return _min_base_font_size;
- }
-
- double getMinConfidenceValue() {
- return _min_confidence_value;
- }
-
- NODE_LABEL_DIRECTION getNodeLabelDirection() {
- return _node_label_direction;
- }
-
- short getNumberOfDigitsAfterCommaForBranchLengthValues() {
- return _number_of_digits_after_comma_for_branch_length_values;
- }
-
- short getNumberOfDigitsAfterCommaForConfidenceValues() {
- return _number_of_digits_after_comma_for_confidence_values;
- }
-
- short getOvMaxHeight() {
- return _ov_max_height;
- }
-
- short getOvMaxWidth() {
- return _ov_max_width;
- }
-
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
- }
-
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
- }
-
- float getPrintLineWidth() {
- return _print_line_width;
- }
-
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- _species_colors = new Hashtable<String, Color>();
- }
- return _species_colors;
- }
-
- Hashtable<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
- }
- return _sequence_colors;
- }
-
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
- }
-
- boolean isAntialiasScreen() {
- if ( ForesterUtil.isMac() ) {
- //Apple Macintosh graphics are slow, turn off anti-alias.
- return false;
- }
- return _antialias_screen;
- }
-
- /**
- * Convenience method.
- *
- * @return true if value in configuration file was 'yes'
- */
- boolean isDrawAsPhylogram() {
- return doCheckOption( display_as_phylogram );
- }
-
- boolean isEditable() {
- return _editable;
- }
-
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isHideControlPanelAndMenubar() {
- return _hide_controls_and_menus;
- }
-
- boolean isInternalNumberAreConfidenceForNhParsing() {
- return _internal_number_are_confidence_for_nh_parsing;
- }
-
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
- }
-
- boolean isShowOverview() {
- return _show_overview;
- }
-
- boolean isShowScale() {
- return _show_scale;
- }
-
- final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
- _ui = UI.NATIVE;
- }
- return _ui == UI.NATIVE;
- }
-
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
- }
-
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
- }
-
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;