import java.awt.Font;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
import org.forester.phylogeny.data.NodeVisualization;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
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 TAXONOMY_EXTRACTION _taxonomy_extraction;
private boolean _editable;
private boolean _background_color_gradient;
private boolean _show_domain_labels;
private boolean _show_default_node_shapes;
private boolean _show_confidence_stddev;
private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style;
+ private NODE_DATA _ext_desc_data_to_return;
private Options() {
init();
_number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
_number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
_nh_parsing_replace_underscores = false;
- _nh_parsing_extract_pfam_taxonomy_codes = false;
+ _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
_cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
_show_domain_labels = true;
setAbbreviateScientificTaxonNames( false );
_color_labels_same_as_parent_branch = false;
_show_confidence_stddev = true;
_nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
+ _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
}
boolean isShowConfidenceStddev() {
return _editable;
}
- final boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
final boolean isGraphicsExportUsingActualSize() {
_editable = editable;
}
- final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
- _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
+ final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
}
final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
- instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
+ instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
.isInternalNumberAreConfidenceForNhParsing() );
}
instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() );
instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() );
+ if ( configuration.getExtDescNodeDataToReturn() != null ) {
+ instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() );
+ }
}
return instance;
}
public static enum PHYLOGENY_GRAPHICS_TYPE {
RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR;
}
+
+ public NodeData.NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
}