&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_COMMON_NAME )
&& ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
if ( extr_taxonomy_pf_only ) {
- ( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
replace_underscores = false;
}
else if ( extr_taxonomy ) {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
replace_underscores = false;
}
}
else {
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
}
( ( NHXParser ) parser ).setReplaceUnderscores( replace_underscores );
( ( NHXParser ) parser ).setIgnoreQuotes( ignore_quotes );