org.biojava.bio.taxa
Class EbiFormat

java.lang.Object
  org.biojava.bio.taxa.EbiFormat

All Implemented Interfaces:

TaxonParser

public class EbiFormat

extends Object

implements TaxonParser

Encapsulate the 'EBI' species format used in Embl, Genbank and Swissprot files. The Taxon objects created by this process have the following annotations:

 key=PROPERTY_NCBI_TAXON, value=String representation of the NCBI taxon id
 key=PROPERTY_TAXON_NAMES, value=Map from name-class to name (see ncbi names.dmp)
 

Author:

Matthew Pocock, Len Trigg

Field Summary

static String	PROPERTY_NCBI_TAXON
static String	PROPERTY_TAXON_NAMES

Constructor Summary

EbiFormat()

Method Summary

static EbiFormat	getInstance()
Taxon	parse(TaxonFactory taxonFactory, String taxonString) Convert a stringified Taxon into a Taxon instance.
String	serialize(Taxon taxon) Convert a Taxon into a stringified representation.
String	serializeSource(Taxon taxon)
String	serializeXRef(Taxon taxon)

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 String PROPERTY_NCBI_TAXON

PROPERTY_TAXON_NAMES

public static final String PROPERTY_TAXON_NAMES

Constructor Detail

EbiFormat

public EbiFormat()

Method Detail

getInstance

public static final EbiFormat getInstance()

parse

public Taxon parse(TaxonFactory taxonFactory,
                   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 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

serializeSource

public String serializeSource(Taxon taxon)

serializeXRef

public String serializeXRef(Taxon taxon)