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;
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;
_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 );
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() );