org.forester.tools

Class PhylogenyDecorator

java.lang.Object

org.forester.tools.PhylogenyDecorator

public final class PhylogenyDecorator
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PhylogenyDecorator.FIELD

Method Summary

Modifier and Type	Method and Description
static void	decorate(Phylogeny phylogeny, Map<String,Map<String,String>> map, boolean picky)
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)
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)
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

Method Detail

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