org.forester.tools
Class PhylogenyDecorator

java.lang.Object
  extended by org.forester.tools.PhylogenyDecorator

public final class PhylogenyDecorator
extends Object


Nested Class Summary
static class PhylogenyDecorator.FIELD
           
 
Field Summary
static boolean SANITIZE
           
static boolean VERBOSE
           
 
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
 

Field Detail

SANITIZE

public static final boolean SANITIZE
See Also:
Constant Field Values

VERBOSE

public static final boolean VERBOSE
See Also:
Constant Field Values
Method Detail

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 values
field -
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 value
field -
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