org.forester.tools
public final class PhylogenyDecorator extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
PhylogenyDecorator.FIELD |
Modifier and Type | Field and Description |
---|---|
static boolean |
SANITIZE |
static boolean |
VERBOSE |
Modifier and Type | Method and Description |
---|---|
static void |
decorate(Phylogeny[] phylogenies,
java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map) |
static void |
decorate(Phylogeny[] phylogenies,
java.util.Map<java.lang.String,java.lang.String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
boolean cut_name_after_space,
boolean process_name_intelligently,
boolean process_similar_to,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
boolean move_domain_numbers_at_end_to_middle) |
static void |
decorate(Phylogeny[] phylogenies,
java.util.Map<java.lang.String,java.lang.String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
java.util.Map<java.lang.String,java.lang.String> intermediate_map,
boolean cut_name_after_space,
boolean process_name_intelligently,
boolean process_similar_to,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
boolean move_domain_numbers_at_end_to_middle) |
static void |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map) |
static void |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.lang.String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
boolean cut_name_after_space,
boolean process_name_intelligently,
boolean process_similar_to,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
boolean move_domain_numbers_at_end_to_middle) |
static void |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.lang.String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
java.util.Map<java.lang.String,java.lang.String> intermediate_map,
boolean cut_name_after_space,
boolean process_name_intelligently,
boolean process_similar_to,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map,
boolean move_domain_numbers_at_end_to_middle) |
static java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> |
parseMappingTable(java.io.File mapping_table_file) |
public static final boolean SANITIZE
public static final boolean VERBOSE
public static void decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky, int numbers_of_chars_allowed_to_remove_if_not_found_in_map) throws java.lang.IllegalArgumentException
java.lang.IllegalArgumentException
public static void decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean picky, boolean cut_name_after_space, boolean process_name_intelligently, boolean process_similar_to, int numbers_of_chars_allowed_to_remove_if_not_found_in_map, boolean move_domain_numbers_at_end_to_middle) throws java.lang.IllegalArgumentException, NHXFormatException
phylogeny
- map
- maps names (in phylogeny) to new valuesfield
- picky
- java.lang.IllegalArgumentException
NHXFormatException
public static void decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean process_name_intelligently, boolean process_similar_to, int numbers_of_chars_allowed_to_remove_if_not_found_in_map, boolean move_domain_numbers_at_end_to_middle) throws java.lang.IllegalArgumentException
phylogeny
- map
- maps names (in phylogeny) to new values if intermediate_map is
null otherwise maps intermediate value to new valuefield
- picky
- intermediate_map
- maps name (in phylogeny) to a intermediate valuejava.lang.IllegalArgumentException
public static void decorate(Phylogeny[] phylogenies, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky, int numbers_of_chars_allowed_to_remove_if_not_found_in_map) throws java.lang.IllegalArgumentException, NHXFormatException
java.lang.IllegalArgumentException
NHXFormatException
public static void decorate(Phylogeny[] phylogenies, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean picky, boolean cut_name_after_space, boolean process_name_intelligently, boolean process_similar_to, int numbers_of_chars_allowed_to_remove_if_not_found_in_map, boolean move_domain_numbers_at_end_to_middle) throws java.lang.IllegalArgumentException, NHXFormatException
java.lang.IllegalArgumentException
NHXFormatException
public static void decorate(Phylogeny[] phylogenies, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean process_name_intelligently, boolean process_similar_to, int numbers_of_chars_allowed_to_remove_if_not_found_in_map, boolean move_domain_numbers_at_end_to_middle) throws java.lang.IllegalArgumentException, NHXFormatException
java.lang.IllegalArgumentException
NHXFormatException
public static java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> parseMappingTable(java.io.File mapping_table_file) throws java.io.IOException
java.io.IOException