&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
replace_underscores = false;
}
else if ( extr_taxonomy ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
replace_underscores = false;
}
}