- static final double MIN_CONFIDENCE_DEFAULT = 0.0;
- private boolean _show_branch_length_values;
- private boolean _internal_number_are_confidence_for_nh_parsing;
- private boolean _show_scale;
- private boolean _show_overview;
- private boolean _antialias_screen;
- private boolean _antialias_print;
- private boolean _graphics_export_visible_only;
- private int _print_size_x;
- private int _print_size_y;
- private double _min_confidence_value;
- private boolean _print_black_and_white;
- private boolean _print_using_actual_size;
- private boolean _graphics_export_using_actual_size;
- private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
- private CLADOGRAM_TYPE _cladogram_type;
- private OVERVIEW_PLACEMENT_TYPE _ov_placement;
- private NODE_LABEL_DIRECTION _node_label_direction;
- private Font _base_font;
- private boolean _match_whole_terms_only;
- private boolean _search_case_sensitive;
- private float _print_line_width;
- private boolean _inverse_search_result;
- private double _scale_bar_length;
- private short _number_of_digits_after_comma_for_confidence_values;
- private short _number_of_digits_after_comma_for_branch_length_values;
- private boolean _nh_parsing_replace_underscores;
- private boolean _nh_parsing_extract_pfam_taxonomy_codes;
- private boolean _editable;
- private boolean _background_color_gradient;
- private boolean _show_domain_labels;
- private boolean _color_labels_same_as_parent_branch;
- private boolean _abbreviate_scientific_names;
- private NodeVisualization.NodeShape _default_node_shape;
- private NodeVisualization.NodeFill _default_node_fill;
- private short _default_node_shape_size;
- private boolean _taxonomy_colorize_node_shapes;
- private boolean _show_default_node_shapes;
+ static final double MIN_CONFIDENCE_DEFAULT = 0.0;
+ private boolean _abbreviate_scientific_names;
+ private boolean _allow_errors_in_distance_to_parent;
+ private boolean _antialias_print;
+ private boolean _antialias_screen;
+ private boolean _background_color_gradient;
+ private Font _base_font;
+ private CLADOGRAM_TYPE _cladogram_type;
+ private boolean _color_by_taxonomic_group;
+ private boolean _color_labels_same_as_parent_branch;
+ private NodeVisualData.NodeFill _default_node_fill;
+ private NodeVisualData.NodeShape _default_node_shape;
+ private short _default_node_shape_size;
+ private boolean _editable;
+ private NodeDataField _ext_desc_data_to_return;
+ private boolean _graphics_export_using_actual_size;
+ private boolean _graphics_export_visible_only;
+ private boolean _internal_number_are_confidence_for_nh_parsing;
+ private boolean _inverse_search_result;
+ private boolean _match_whole_terms_only;
+ private boolean _search_with_regex;
+ private double _min_confidence_value;
+ private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
+ private boolean _nh_parsing_replace_underscores;
+ private NODE_LABEL_DIRECTION _node_label_direction;
+ private short _number_of_digits_after_comma_for_branch_length_values;
+ private short _number_of_digits_after_comma_for_confidence_values;
+ private OVERVIEW_PLACEMENT_TYPE _ov_placement;
+ private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type;
+ private boolean _print_black_and_white;
+ private float _print_line_width;
+ private int _print_size_x;
+ private int _print_size_y;
+ private boolean _print_using_actual_size;
+ private double _scale_bar_length;
+ private boolean _search_case_sensitive;
+ private boolean _show_annotation_ref_source;
+ private boolean _show_confidence_stddev;
+ private boolean _show_default_node_shapes_for_marked_nodes;
+ private boolean _show_default_node_shapes_external;
+ private boolean _show_default_node_shapes_internal;
+ private boolean _show_domain_labels;
+ private boolean _show_overview;
+ private boolean _show_scale;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction;
+ private boolean _line_up_renderable_node_data;
+ private boolean _right_align_domains;