import java.awt.Font;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.util.ForesterUtil;
/*
*/
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 NodeShape _default_node_shape;
- private 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 _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 Options() {
init();
}
final private void init() {
- _default_node_shape = NodeShape.NONE;
+ _default_node_shape = NodeShape.CIRCLE;
_default_node_fill = NodeFill.GRADIENT;
_default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
_taxonomy_colorize_node_shapes = false;
return new Options();
}
- boolean isShowDefaultNodeShapes() {
- return _show_default_node_shapes;
- }
- void setShowDefaultNodeShapes(boolean show_default_node_shapes) {
- _show_default_node_shapes = show_default_node_shapes;
+ boolean isShowDefaultNodeShapes() {
+ return _show_default_node_shapes;
}
- final static Options createInstance( final Configuration configuration ) {
+
+ void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) {
+ _show_default_node_shapes = show_default_node_shapes;
+ }
+
+ public final static Options createInstance( final Configuration configuration ) {
final Options instance = createDefaultInstance();
if ( configuration != null ) {
instance.setAntialiasScreen( configuration.isAntialiasScreen() );
if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
}
- instance.setTaxonomyColorizeNodeShapes( configuration
- .isTaxonomyColorizeNodeShapes() );
+ instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
}
return instance;
HORIZONTAL, RADIAL;
}
- enum NodeFill {
- NONE, GRADIENT, SOLID
- }
-
- enum NodeShape {
- NONE, CIRCLE, RECTANGLE
- }
-
static enum OVERVIEW_PLACEMENT_TYPE {
UPPER_LEFT( "upper left" ),
UPPER_RIGHT( "upper right" ),