public final class PhylogenyDecorator
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
PhylogenyDecorator.FIELD |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.lang.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 java.lang.String |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.lang.String> map,
PhylogenyDecorator.FIELD field,
boolean extract_bracketed_scientific_name,
boolean extract_bracketed_tax_code,
boolean picky,
java.util.Map<java.lang.String,java.lang.String> intermediate_map,
boolean cut_name_after_space,
boolean trim_after_tilde,
boolean verbose) |
|
static void |
decorate(Phylogeny phylogeny,
java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map,
boolean picky) |
|
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 void decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> map, boolean picky) throws java.lang.IllegalArgumentException, PhyloXmlDataFormatException
java.lang.IllegalArgumentException
PhyloXmlDataFormatException
public static java.lang.String decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.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 java.lang.IllegalArgumentException, NHXFormatException, PhyloXmlDataFormatException
java.lang.IllegalArgumentException
NHXFormatException
PhyloXmlDataFormatException
public static java.lang.String decorate(Phylogeny phylogeny, java.util.Map<java.lang.String,java.lang.String> map, PhylogenyDecorator.FIELD field, boolean extract_bracketed_scientific_name, boolean extract_bracketed_tax_code, boolean picky, java.util.Map<java.lang.String,java.lang.String> intermediate_map, boolean cut_name_after_space, boolean trim_after_tilde, boolean verbose) throws java.lang.IllegalArgumentException, PhyloXmlDataFormatException
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
PhyloXmlDataFormatException
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