- }
-
- private final static String addTildeAnnotation( final String tilde_annotation, final String new_value ) {
- if ( ForesterUtil.isEmpty( tilde_annotation ) ) {
- return new_value;
- }
- return new_value + tilde_annotation;
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, Map<String, String>> map,
- final boolean picky,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map )
- throws IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator
- .decorate( phylogenie, map, picky, numbers_of_chars_allowed_to_remove_if_not_found_in_map );
- }
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator.decorate( phylogenie,
- map,
- field,
- extract_bracketed_scientific_name,
- extract_bracketed_tax_code,
- picky,
- cut_name_after_space,
- process_name_intelligently,
- process_similar_to,
- numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- trim_after_tilde );
- }
- }
-
- public static void decorate( final Phylogeny[] phylogenies,
- final Map<String, String> map,
- final FIELD field,
- final boolean extract_bracketed_scientific_name,
- final boolean extract_bracketed_tax_code,
- final boolean picky,
- final Map<String, String> intermediate_map,
- final boolean cut_name_after_space,
- final boolean process_name_intelligently,
- final boolean process_similar_to,
- final int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- final boolean trim_after_tilde ) throws IllegalArgumentException, NHXFormatException,
- PhyloXmlDataFormatException {
- for( final Phylogeny phylogenie : phylogenies ) {
- PhylogenyDecorator.decorate( phylogenie,
- map,
- field,
- extract_bracketed_scientific_name,
- extract_bracketed_tax_code,
- picky,
- intermediate_map,
- cut_name_after_space,
- process_name_intelligently,
- process_similar_to,
- numbers_of_chars_allowed_to_remove_if_not_found_in_map,
- trim_after_tilde );
- }