final public class Options {
static final double MIN_CONFIDENCE_DEFAULT = 0.0;
+ private boolean _color_by_taxonomic_group;
private boolean _show_branch_length_values;
private boolean _internal_number_are_confidence_for_nh_parsing;
private boolean _show_scale;
private boolean _editable;
private boolean _background_color_gradient;
private boolean _show_domain_labels;
+ private boolean _show_annotation_ref_source;
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_internal;
private boolean _show_default_node_shapes_external;
private boolean _show_confidence_stddev;
return _show_domain_labels;
}
+ public final boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
+ _show_annotation_ref_source = show_annotation_ref_source;
+ }
+
public void setBackgroundColorGradient( final boolean background_color_gradient ) {
_background_color_gradient = background_color_gradient;
}
return _show_branch_length_values;
}
+ final boolean isColorByTaxonomicGroup() {
+ return _color_by_taxonomic_group;
+ }
+
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
return _show_scale;
}
- boolean isTaxonomyColorizeNodeShapes() {
- return _taxonomy_colorize_node_shapes;
- }
-
final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
_abbreviate_scientific_names = abbreviate_scientific_names;
}
_show_branch_length_values = show_branch_length_values;
}
+ final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) {
+ _color_by_taxonomic_group = color_by_taxonomic_group;
+ }
+
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
_show_scale = show_scale;
}
- void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) {
- _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes;
- }
-
- final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
_taxonomy_extraction = taxonomy_extraction;
}
_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;
_show_branch_length_values = false;
_internal_number_are_confidence_for_nh_parsing = false;
_show_scale = false;
- _antialias_screen = false;
+ _antialias_screen = true;
_antialias_print = true;
_graphics_export_visible_only = false;
_editable = true;
_taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
_cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
_show_domain_labels = true;
+ _show_annotation_ref_source = true;
setAbbreviateScientificTaxonNames( false );
_color_labels_same_as_parent_branch = false;
_show_confidence_stddev = true;
instance.setShowScale( configuration.isShowScale() );
instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
instance.setShowOverview( configuration.isShowOverview() );
+ instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
instance.setCladogramType( configuration.getCladogramType() );
instance.setOvPlacement( configuration.getOvPlacement() );
instance.setPrintLineWidth( configuration.getPrintLineWidth() );
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
- instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
+ instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
.isInternalNumberAreConfidenceForNhParsing() );
instance.setEditable( configuration.isEditable() );
instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
instance.setShowDomainLabels( configuration.isShowDomainLabels() );
+ instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() );
instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() );
if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) {
instance.setMinConfidenceValue( configuration.getMinConfidenceValue() );
if ( configuration.getDefaultNodeShapeSize() >= 0 ) {
instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() );
}
- instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() );
instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() );
if ( configuration.getExtDescNodeDataToReturn() != null ) {