org.biojava.bio.taxa
Class EbiFormat

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

Deprecated. replaced by classes in org.biojavax.bio.taxa

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

PROPERTY_TAXON_NAMES

public static final String PROPERTY_TAXON_NAMES
Deprecated. 
Constructor Detail

EbiFormat

public EbiFormat()
Deprecated. 
Method Detail

getInstance

public static final EbiFormat getInstance()
Deprecated. 

parse

public Taxon parse(TaxonFactory taxonFactory,
                   String taxonString)
            throws ChangeVetoException,
                   CircularReferenceException
Deprecated. 
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)
Deprecated. 
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)
Deprecated. 

serializeXRef

public String serializeXRef(Taxon taxon)
Deprecated.