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java.lang.Objectorg.biojava.bio.taxa.EbiFormat
org.biojavax.bio.taxa
public class EbiFormat
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)
Field Summary | |
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static String |
PROPERTY_NCBI_TAXON
Deprecated. |
static String |
PROPERTY_TAXON_NAMES
Deprecated. |
Constructor Summary | |
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EbiFormat()
Deprecated. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String PROPERTY_NCBI_TAXON
public static final String PROPERTY_TAXON_NAMES
Constructor Detail |
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public EbiFormat()
Method Detail |
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public static final EbiFormat getInstance()
public Taxon parse(TaxonFactory taxonFactory, String taxonString) throws ChangeVetoException, CircularReferenceException
TaxonParser
parse
in interface TaxonParser
taxonFactory
- the TaxonFactory used to instantiate taxa instancestaxonString
- the String to parse
ChangeVetoException
CircularReferenceException
public String serialize(Taxon taxon)
TaxonParser
serialize
in interface TaxonParser
taxon
- the Taxon to serialize
public String serializeSource(Taxon taxon)
public String serializeXRef(Taxon taxon)
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