+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
+ }
+
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
+ }
+
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
+ }
+
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
+ }
+
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
+ }
+
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
+ }
+
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
+ }
+
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ }
+
+ public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
+ _show_branch_length_values = show_branch_length_values;
+ }
+
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
+ }
+
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ }
+
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
+ }
+
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
+ }
+
+ public void setTaxonomyColorize( final boolean b ) {
+ display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
+ _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
+ }
+
+ public void setUseBranchesWidths( final boolean b ) {
+ display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
+ }
+
+ 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;
+ }
+
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
+ }
+
+ int getMaxBaseFontSize() {
+ return _max_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;
+ }
+
+ 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;
+ }