org.forester.tools
Class PhylogenyDecorator
java.lang.Object
org.forester.tools.PhylogenyDecorator
public final class PhylogenyDecorator
- extends Object
Method Summary |
static void |
decorate(Phylogeny[] phylogenies,
Map<String,Map<String,String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map)
|
static void |
decorate(Phylogeny[] phylogenies,
Map<String,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,
Map<String,String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
Map<String,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,
Map<String,Map<String,String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map)
|
static void |
decorate(Phylogeny phylogeny,
Map<String,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,
Map<String,String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
Map<String,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 Map<String,Map<String,String>> |
parseMappingTable(File mapping_table_file)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SANITIZE
public static final boolean SANITIZE
- See Also:
- Constant Field Values
VERBOSE
public static final boolean VERBOSE
- See Also:
- Constant Field Values
decorate
public static void decorate(Phylogeny phylogeny,
Map<String,Map<String,String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map)
throws IllegalArgumentException
- Throws:
IllegalArgumentException
decorate
public static void decorate(Phylogeny phylogeny,
Map<String,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 IllegalArgumentException,
NHXFormatException
- Parameters:
phylogeny
- map
- maps names (in phylogeny) to new valuesfield
- picky
-
- Throws:
IllegalArgumentException
NHXFormatException
decorate
public static void decorate(Phylogeny phylogeny,
Map<String,String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
Map<String,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 IllegalArgumentException
- Parameters:
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 value
- Throws:
IllegalArgumentException
decorate
public static void decorate(Phylogeny[] phylogenies,
Map<String,Map<String,String>> map,
boolean picky,
int numbers_of_chars_allowed_to_remove_if_not_found_in_map)
throws IllegalArgumentException,
NHXFormatException
- Throws:
IllegalArgumentException
NHXFormatException
decorate
public static void decorate(Phylogeny[] phylogenies,
Map<String,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 IllegalArgumentException,
NHXFormatException
- Throws:
IllegalArgumentException
NHXFormatException
decorate
public static void decorate(Phylogeny[] phylogenies,
Map<String,String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean picky,
Map<String,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 IllegalArgumentException,
NHXFormatException
- Throws:
IllegalArgumentException
NHXFormatException
parseMappingTable
public static Map<String,Map<String,String>> parseMappingTable(File mapping_table_file)
throws IOException
- Throws:
IOException