- static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
- private static final String DISPLAY_COLOR_KEY = "display_color";
- private static final int DEPRECATED = -2;
- private UI _ui = UI.UNKNOWN;
- private boolean _use_tabbed_display = false;
- private boolean _hide_controls_and_menus = false;
- private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- private SortedMap<String, Color> _display_colors = null;
- private boolean _antialias_screen = true;
- private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private String _base_font_family_name = "";
- private int _base_font_size = -1;
- private int _min_base_font_size = 2;
- private int _max_base_font_size = 20;
- private int _graphics_export_x = -1;
- private int _graphics_export_y = -1;
- private short _ov_max_width = 80;
- private short _ov_max_height = 80;
- private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
- private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
- private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
- private boolean _show_scale = false;
- private boolean _show_branch_length_values = false;
- private boolean _show_overview = true;
- private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
- private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
- private boolean _editable = true;
- private boolean _nh_parsing_replace_underscores = false;
- private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
- private boolean _internal_number_are_confidence_for_nh_parsing = false;
- private boolean _display_sequence_relations = false;
- private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
- private boolean _background_color_gradient = false;
- private boolean _show_domain_labels = true;
- private boolean _show_annotation_ref_source = true;
- private boolean _abbreviate_scientific_names = false;
- private boolean _color_labels_same_as_parent_branch = false;
- private boolean _show_default_node_shapes_internal = false;
- private boolean _show_default_node_shapes_external = false;
- private NodeShape _default_node_shape = NodeShape.RECTANGLE;
- private NodeFill _default_node_fill = NodeFill.SOLID;
- private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- private boolean _taxonomy_colorize_node_shapes = false;
- private int _default_bootstrap_samples = -1;
- private File _path_to_local_mafft = null;
- private File _path_to_local_fastme = null;
- private File _path_to_local_raxml = null;
- final static int display_as_phylogram = 0;
- final static int show_node_names = 1;
- final static int show_tax_code = 2;
- final static int show_annotation = 3;
- final static int write_confidence_values = 4;
- final static int write_events = 5;
+ final static int add_new_node = 14;
+ final static int blast = 9;
+ final static String clickto_options[][] = {
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" },
+ { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
+ { "Open Taxonomy DB", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" },
+ { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
+ { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
+ { "Return", "display" }, { "Select Node(s)", "display" } };
+ final static int collapse_uncollapse = 1;
+ final static int color_according_to_annotation = 19;