public final class Configuration {
- 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;
final static int color_according_to_species = 6;
final static int color_branches = 7;
- final static int width_branches = 8;
- final static int show_custom_node_shapes = 9;
- final static int show_domain_architectures = 10;
- final static int show_binary_characters = 11;
- final static int show_binary_character_counts = 12;
- final static int show_seq_names = 13;
- final static int show_sequence_acc = 14;
+ final static int color_subtree = 5;
+ final static int copy_subtree = 11;
+ final static int cut_subtree = 10;
+ final static int delete_subtree_or_node = 13;
+ final static int display_as_phylogram = 0;
final static int display_internal_data = 15;
- final static int dynamically_hide_data = 16;
- final static int show_taxonomy_scientific_names = 17;
- final static int show_taxonomy_common_names = 18;
- final static int color_according_to_annotation = 19;
- final static int show_seq_symbols = 20;
- final static int node_data_popup = 21;
- final static int show_relation_confidence = 22;
- final static int show_vector_data = 23;
- final static int show_taxonomy_images = 24;
- final static int show_properties = 25;
- final static int show_gene_names = 26;
// ------------------
// Click-to options
// ------------------
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_subtree = 5;
- final static int open_seq_web = 6;
- final static int open_pdb_web = 7;
- final static int open_tax_web = 8;
- final static int blast = 9;
- final static int cut_subtree = 10;
- final static int copy_subtree = 11;
- final static int paste_subtree = 12;
- final static int delete_subtree_or_node = 13;
- final static int add_new_node = 14;
- final static int edit_node_data = 15;
- final static int sort_descendents = 16;
- final static int get_ext_desc_data = 17;
- final static int select_nodes = 18;
- // ---------------------------
- // Display options for trees
- // ---------------------------
- // ---------------------------------
- // Pertaining to the config itself
- // ---------------------------------
- // Full path to config (may be URL)
- String config_filename;
- String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
final static String display_options[][] = {
{ "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
{ "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
- { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "yes" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
{ "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" },
{ "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" },
{ "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
{ "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
{ "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
{ "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } };
- 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 dynamically_hide_data = 16;
+ final static int edit_node_data = 15;
+ final static int get_ext_desc_data = 17;
+ final static int node_data_popup = 21;
+ final static int open_pdb_web = 7;
+ final static int open_seq_web = 6;
+ final static int open_tax_web = 8;
+ final static int paste_subtree = 12;
+ final static int reroot = 2;
+ final static int select_nodes = 18;
+ final static int show_annotation = 3;
+ final static int show_binary_character_counts = 12;
+ final static int show_binary_characters = 11;
+ final static int show_custom_node_shapes = 9;
+ final static int show_domain_architectures = 10;
+ final static int show_gene_names = 26;
+ final static int show_node_names = 1;
+ final static int show_properties = 25;
+ final static int show_relation_confidence = 22;
+ final static int show_seq_names = 13;
+ final static int show_seq_symbols = 20;
+ final static int show_sequence_acc = 14;
+ final static int show_tax_code = 2;
+ final static int show_taxonomy_common_names = 18;
+ final static int show_taxonomy_images = 24;
+ final static int show_taxonomy_scientific_names = 17;
+ final static int show_vector_data = 23;
+ final static int sort_descendents = 16;
+ final static int subtree = 3;
+ final static int swap = 4;
+ static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
+ final static int width_branches = 8;
+ final static int write_confidence_values = 4;
+ final static int write_events = 5;
+ // ----------------
+ // Function colors
+ // ----------------
+ private static Hashtable<String, Color> _annotation_colors;
+ // ----------------
+ // Domain colors
+ // ----------------
+ private static Hashtable<String, Color> _domain_colors;
+ // ----------------
+ // Species colors
+ // ----------------
+ private static Hashtable<String, Color> _species_colors;
+ private static String DEFAULT_FONT_FAMILY = "";
+ private static final int DEPRECATED = -2;
+ private static final String DISPLAY_COLOR_KEY = "display_color";
+ // ---------------------------
+ // Display options for trees
+ // ---------------------------
+ // ---------------------------------
+ // Pertaining to the config itself
+ // ---------------------------------
+ // Full path to config (may be URL)
+ String config_filename;
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
+ String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
// --------------
// Color set
// --------------
// Fonts
// -------
TreeFontSet tree_font_set;
- // ----------------
- // Species colors
- // ----------------
- private static Hashtable<String, Color> _species_colors;
- // ----------------
- // Domain colors
- // ----------------
- private static Hashtable<String, Color> _domain_colors;
- // ----------------
- // Function colors
- // ----------------
- private static Hashtable<String, Color> _annotation_colors;
boolean verbose = Constants.VERBOSE_DEFAULT;
- private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
- private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
- private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
- private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
- private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
- private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
- private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
- private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
- private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
- private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
+ private boolean _abbreviate_scientific_names = false;
+ private boolean _antialias_screen = true;
+ private boolean _background_color_gradient = false;
+ private String _base_font_family_name = "";
+ private int _base_font_size = -1;
+ private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+ private boolean _color_labels_same_as_parent_branch = false;
+ private int _default_bootstrap_samples = -1;
+ private NodeFill _default_node_fill = NodeFill.SOLID;
+ private NodeShape _default_node_shape = NodeShape.RECTANGLE;
+ private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ private SortedMap<String, Color> _display_colors = null;
+ private boolean _display_sequence_relations = false;
private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
+ private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
+ private boolean _editable = true;
private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
- private String _label_for_get_ext_descendents_data = "";
private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
private int _frame_x_size;
private int _frame_y_size;
+ private int _graphics_export_x = -1;
+ private int _graphics_export_y = -1;
+ private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
+ private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
+ private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
+ private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
+ private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
+ private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
+ private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
+ private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
+ private boolean _hide_controls_and_menus = false;
+ private boolean _internal_number_are_confidence_for_nh_parsing = false;
+ private String _label_for_get_ext_descendents_data = "";
+ private int _max_base_font_size = 20;
private boolean _midpoint_root = false;
- private static String DEFAULT_FONT_FAMILY = "";
+ private int _min_base_font_size = 2;
+ private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
+ private boolean _nh_parsing_replace_underscores = false;
+ private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
+ private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+ private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
+ private short _ov_max_height = 80;
+ private short _ov_max_width = 80;
+ private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
+ private File _path_to_local_fastme = null;
+ private File _path_to_local_mafft = null;
+ private File _path_to_local_raxml = null;
+ private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
+ private boolean _show_annotation_ref_source = true;
+ private boolean _show_branch_length_values = false;
+ private boolean _show_default_node_shapes_external = false;
+ private boolean _show_default_node_shapes_internal = false;
+ private boolean _show_domain_labels = true;
+ private boolean _show_overview = true;
+ private boolean _show_scale = false;
+ private boolean _taxonomy_colorize_node_shapes = false;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
+ private UI _ui = UI.UNKNOWN;
+ private boolean _use_tabbed_display = false;
+ private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
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;
}
_base_font_size = base_font_size;
}
- private void setMaxBaseFontSize( final int max_base_font_size ) {
- _max_base_font_size = max_base_font_size;
- }
-
- private void setMinBaseFontSize( final int min_base_font_size ) {
- _min_base_font_size = min_base_font_size;
- }
-
public void setColorizeBranches( final boolean b ) {
display_options[ color_branches ][ 2 ] = b ? "yes" : "no";
}
_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;
}
return _base_font_size;
}
- int getMinBaseFontSize() {
- return _min_base_font_size;
- }
-
- int getMaxBaseFontSize() {
- return _max_base_font_size;
- }
-
CLADOGRAM_TYPE getCladogramType() {
return _cladogram_type;
}
return _gui_menu_text_color;
}
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
+ }
+
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
+ }
+
double getMinConfidenceValue() {
return _min_confidence_value;
}
}
}
- private void setShowAnnotationRefSource( final boolean b ) {
- _show_annotation_ref_source = b;
- }
-
private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
_label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
+ }
+
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
+ }
+
private void setOvMaxHeight( final short ov_max_height ) {
_ov_max_height = ov_max_height;
}
_path_to_local_raxml = path_to_local_raxml;
}
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
+ }
+
private void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
}
public enum EXT_NODE_DATA_RETURN_ON {
- CONSOLE, WINODW, BUFFER_ONLY;
+ BUFFER_ONLY, CONSOLE, WINODW;
}
public enum UI {
- NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
}
static enum TRIPLET {
- TRUE, FALSE, UNKNOWN
- }
-
- public boolean isMidpointReroot() {
- return _midpoint_root;
- }
-
- public void setMidpointReroot( final boolean midpoint_root ) {
- _midpoint_root = midpoint_root;
- }
-
- public boolean isShowAnnotationRefSource() {
- return _show_annotation_ref_source;
- }
-
- public boolean isColorByTaxonomicGroup() {
- return false;
+ FALSE, TRUE, UNKNOWN
}
}
*/
public final class TreeColorSet {
- public static final String OVERVIEW = "Overview";
public static final String ANNOTATION = "Annotation";
+ public static final String BACKGROUND = "Background";
+ public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
public static final String BINARY_DOMAIN_COMBINATIONS = "Binary Domain Combinations";
- public static final String DOMAINS = "Domains";
- public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
- public static final String SPECIATION = "Speciation";
- public static final String DUPLICATION = "Duplication";
- public static final String MATCHING_NODES = "Matching Nodes";
- public static final String COLLAPSED = "Collapsed";
- public static final String NODE_BOX = "Node Box";
public static final String BRANCH = "Branch";
public static final String BRANCH_LENGTH = "Branch Length";
+ public static final String COLLAPSED = "Collapsed";
public static final String CONFIDENCE = "Confidence";
- public static final String TAXONOMY = "Taxonomy";
+ public static final String DOMAINS = "Domains";
+ public static final String DUPLICATION = "Duplication";
+ public static final String DUPLICATION_OR_SPECATION = "Duplication or Specation";
+ public static final String MATCHING_NODES_A = "Matching A";
+ public static final String MATCHING_NODES_A_AND_B = "Matching A and B";
+ public static final String MATCHING_NODES_B = "Matching B";
+ public static final String NODE_BOX = "Node Box";
+ public static final String OVERVIEW = "Overview";
public static final String SEQUENCE = "Sequence";
- public static final String BACKGROUND_GRADIENT_BOTTOM = "Background Gradient Bottom";
- public static final String BACKGROUND = "Background";
- static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver",
- "The Matrix", "White & Blue", "Cyan", "Clockwork", "Blue", "Blue & White", "Neon" };
+ public static final String SPECIATION = "Speciation";
+ public static final String TAXONOMY = "Taxonomy";
static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
- TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES, DUPLICATION, SPECIATION,
- DUPLICATION_OR_SPECATION, DOMAINS, BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
+ TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
+ MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAINS,
+ BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
+ static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
+ "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
+ // Color schemes:
+ private int _color_scheme;
// All the color sets; better be the same # of sets as there are names!
private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
new Color( 0, 100, 100 ), // background_color_gradient_bottom
- new Color( 220, 220, 220 ), // sequence __ Default (same as Black)
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 56, 176, 222 ), // support
+ new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
+ new Color( 255, 220, 220 ), // taxonomy
+ new Color( 56, 176, 255 ), // support
new Color( 140, 140, 140 ), // branch_length_color
new Color( 255, 255, 255 ), // branch_color
new Color( 255, 255, 255 ), // box_color
, new Color( 130, 130, 130 ) // overview
}, { new Color( 0, 0, 0 ), // background_color
new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 220, 220, 220 ), // sequence __ Black
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 56, 176, 222 ), // support
+ new Color( 230, 230, 230 ), // sequence __ Black
+ new Color( 255, 220, 220 ), // taxonomy
+ new Color( 56, 176, 255 ), // support
new Color( 140, 140, 140 ), // branch_length_color
new Color( 255, 255, 255 ), // branch_color
new Color( 255, 255, 255 ), // box_color
new Color( 27, 255, 0 ) // annotation
, new Color( 77, 77, 255 ) // ov
} };
- // Color schemes:
- private int _color_scheme;
- // The drawing colors
- private Color seq_color;
- private Color taxonomy_color;
- private Color bootstrap_color;
- private Color branch_length_color;
- private Color branch_color;
- private Color box_color;
+ private Color annotation_color;
private Color background_color;
private Color background_color_gradient_bottom;
- private Color dup_box_color;
- private Color spec_box_color;
+ private Color binary_domain_combinations_color;
+ private Color bootstrap_color;
+ private Color box_color;
+ private Color branch_color;
+ private Color branch_length_color;
private Color collapse_fill_color;
+ private Color domains_color;
+ private Color dup_box_color;
+ private Color duplication_or_specation_color;
private Color found_color_0;
- private Color found_color_1;
private Color found_color_0_and_1;
- private Color duplication_or_specation_color;
- private Color domains_color;
- private Color binary_domain_combinations_color;
- private Color annotation_color;
+ private Color found_color_1;
private Color ov_color;
+ // The drawing colors
+ private Color seq_color;
+ private Color spec_box_color;
+ private Color taxonomy_color;
private TreeColorSet() {
// Hidden constructor.
return found_color_0;
}
- Color getFoundColor1() {
- return found_color_1;
- }
-
Color getFoundColor0and1() {
return found_color_0_and_1;
}
+ Color getFoundColor1() {
+ return found_color_1;
+ }
+
Color getGainedCharactersColor() {
return Color.GREEN;
}
}
}
- private void setColorForDefault( final int i, final Color color ) {
- _color_schemes[ 0 ][ i ] = color;
- }
-
/**
* Switches colors between different schemes.
*/
_color_scheme = color_scheme;
}
+ private void setColorForDefault( final int i, final Color color ) {
+ _color_schemes[ 0 ][ i ] = color;
+ }
+
static TreeColorSet createInstance() {
final TreeColorSet tcs = new TreeColorSet();
tcs.setColorSchema( 0 );
git://source.jalview.org / jalview.git / commitdiff