org.forester.tools
Class PhylogenyDecorator

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

public final class PhylogenyDecorator
extends java.lang.Object

Nested Class Summary

static class

PhylogenyDecorator.FIELD

Field Summary

static boolean	SANITIZE
static boolean	VERBOSE

Method Summary

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)

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,
                            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,
                            PhyloXmlDataFormatException

Throws:

java.lang.IllegalArgumentException

PhyloXmlDataFormatException

decorate

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,
                            PhyloXmlDataFormatException

Parameters:

phylogeny -

map - maps names (in phylogeny) to new values

field -

picky -

Throws:

java.lang.IllegalArgumentException

NHXFormatException

PhyloXmlDataFormatException

decorate

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,
                            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:

java.lang.IllegalArgumentException

PhyloXmlDataFormatException

decorate

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,
                            PhyloXmlDataFormatException

Throws:

java.lang.IllegalArgumentException

NHXFormatException

PhyloXmlDataFormatException

decorate

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,
                            PhyloXmlDataFormatException

Throws:

java.lang.IllegalArgumentException

NHXFormatException

PhyloXmlDataFormatException

decorate

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,
                            PhyloXmlDataFormatException

Throws:

java.lang.IllegalArgumentException

NHXFormatException

PhyloXmlDataFormatException

parseMappingTable

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

Throws:

java.io.IOException