import java.awt.Font;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.NodeVisualization;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
*/
final public class Options {
- 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;
- private boolean _show_confidence_stddev;
- private boolean _use_brackets_for_conf_in_nh_export;
+ 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;
+ private boolean _show_confidence_stddev;
+ private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
private Options() {
init();
setAbbreviateScientificTaxonNames( false );
_color_labels_same_as_parent_branch = false;
_show_confidence_stddev = true;
- _use_brackets_for_conf_in_nh_export = false;
+ _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
}
boolean isShowConfidenceStddev() {
_show_confidence_stddev = show_confidence_stddev;
}
- boolean isUseBracketsForConfInNhExport() {
- return _use_brackets_for_conf_in_nh_export;
+ NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() {
+ return _nh_conversion_support_value_style;
}
- void setUseBracketsForConfInNhExport( final boolean use_brackets_for_conf_in_nh_export ) {
- _use_brackets_for_conf_in_nh_export = use_brackets_for_conf_in_nh_export;
+ void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) {
+ _nh_conversion_support_value_style = nh_conversion_support_value_style;
}
final boolean isAbbreviateScientificTaxonNames() {