Class PhylogenyDecorator

Method Details

• decorate

  public static void decorate(Phylogeny phylogeny, Map<String,Map<String,String>> map, boolean picky) throws IllegalArgumentException, PhyloXmlDataFormatException

  Throws:

  IllegalArgumentException

  PhyloXmlDataFormatException

• decorate

  public static String decorate(Phylogeny phylogeny, Map<String,String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) throws IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException

  Throws:

  IllegalArgumentException

  NHXFormatException

  PhyloXmlDataFormatException

• decorate

  public static String decorate(Phylogeny phylogeny, Map<String,String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, Map<String,String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) throws IllegalArgumentException, PhyloXmlDataFormatException

  Parameters:

  phylogeny -

  map - maps names (in phylogeny) to new values if intermediate_map is null otherwise maps intermediate value to new value

  field -

  picky -

  intermediate_map - maps name (in phylogeny) to a intermediate value

  Throws:

  IllegalArgumentException

  PhyloXmlDataFormatException

• parseMappingTable

  public static Map<String,Map<String,String>> parseMappingTable(File mapping_table_file) throws IOException

  Throws:

  IOException