- static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
- private static final String WEB_LINK_KEY = "web_link";
- 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, WebLink> _weblinks = null;
- 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 _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.PFAM_STYLE_ONLY;
- 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 _abbreviate_scientific_names = false;
- private boolean _color_labels_same_as_parent_branch = false;
- private boolean _show_default_node_shapes = false;
- private NodeShape _default_node_shape = NodeShape.CIRCLE;
- private NodeFill _default_node_fill = NodeFill.GRADIENT;
- 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;
- private File _path_to_local_clustalo = null;
+
+ public enum UI {
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ }
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
+ final static String clickto_options[][] = {
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
+ { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
+ { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
+ { "Open Taxonomy DB", "display" }, { "Launch 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" },
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } };
+ private final static String DEFAULT_SPECIES_COLORS[][] = {
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
+ final static int display_node_data = 0;
+ final static int collapse_uncollapse = 1;
+ final static int reroot = 2;
+ final static int subtree = 3;
+ final static int swap = 4;
+ final static int color_node_font = 5;
+ final static int change_node_font = 6;
+ final static int color_subtree = 7;
+ final static int open_seq_web = 8;
+ final static int open_pdb_web = 9;
+ final static int open_tax_web = 10;
+ final static int blast = 11;
+ final static int cut_subtree = 12;
+ final static int copy_subtree = 13;
+ final static int paste_subtree = 14;
+ final static int delete_subtree_or_node = 15;
+ final static int add_new_node = 16;
+ final static int edit_node_data = 17;
+ final static int sort_descendents = 18;
+ final static int get_ext_desc_data = 19;
+ final static int select_nodes = 20;
+ // ------------------
+ // Click-to options
+ // ------------------
+ final static String display_options[][] = {
+ { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
+ { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+ { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
+ { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
+ { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+ { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
+ { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+ { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+ { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
+ { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+ { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+ { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };