+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
+ }
+
+ public int getFrameXSize() {
+ return _frame_x_size;
+ }
+
+ public int getFrameYSize() {
+ return _frame_y_size;
+ }
+
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
+ }
+
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
+ }
+
+ public File getpathToLocalMafft() {
+ return _path_to_local_mafft;
+ }
+
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
+ }
+
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
+ }
+
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
+ }
+
+ public boolean isColorByTaxonomicGroup() {
+ return false;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
+ }
+
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
+ }
+
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
+ }
+
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
+ }
+
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
+ }
+
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
+ }
+
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
+ }
+
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
+ }
+
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ }
+
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
+ }
+
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
+ }
+
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
+ }
+
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
+ }
+
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_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_seq_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 setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
+ }
+
+ 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 setUseBranchesWidths( final boolean b ) {
+ display_options[ width_branches ][ 2 ] = b ? "yes" : "no";