- else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
- final boolean e = parseBoolean( ( String ) st.nextElement() );
- if ( e && isReplaceUnderscoresInNhParsing() ) {
+ else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
+ final String s = ( String ) st.nextElement();
+ if ( s.equalsIgnoreCase( "no" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
+ else if ( s.equalsIgnoreCase( "yes" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+ }
+ else if ( s.equalsIgnoreCase( "pfam" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+ }
+ if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {