org.biojava.bio.taxa
Class EbiFormat

java.lang.Object
  extended byorg.biojava.bio.taxa.EbiFormat
All Implemented Interfaces:
TaxonParser

public class EbiFormat
extends java.lang.Object
implements TaxonParser

Encapsulate the 'EBI' species format used in Embl, Genbank and Swissprot files.

Author:
Matthew Pocock

Field Summary
static java.lang.String PROPERTY_NCBI_TAXON
           
 
Constructor Summary
EbiFormat()
           
 
Method Summary
static EbiFormat getInstance()
           
 Taxon parse(TaxonFactory taxonFactory, java.lang.String taxonString)
          Convert a stringified Taxon into a Taxon instance.
 java.lang.String serialize(Taxon taxon)
          Convert a Taxon into a stringified representation.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

PROPERTY_NCBI_TAXON

public static final java.lang.String PROPERTY_NCBI_TAXON
Constructor Detail

EbiFormat

public EbiFormat()
Method Detail

getInstance

public static final EbiFormat getInstance()

parse

public Taxon parse(TaxonFactory taxonFactory,
                   java.lang.String taxonString)
            throws ChangeVetoException,
                   CircularReferenceException
Description copied from interface: TaxonParser
Convert a stringified Taxon into a Taxon instance.

Specified by:
parse in interface TaxonParser
Parameters:
taxonFactory - the TaxonFactory used to instantiate taxa instances
taxonString - the String to parse
Returns:
a Taxon instance created by the TaxonFactory from the taxonString
Throws:
ChangeVetoException
CircularReferenceException

serialize

public java.lang.String serialize(Taxon taxon)
Description copied from interface: TaxonParser
Convert a Taxon into a stringified representation.

Specified by:
serialize in interface TaxonParser
Parameters:
taxon - the Taxon to serialize
Returns:
the stringified version of Taxon