Package org.biojava.bio.taxa
Class EbiFormat
java.lang.Object
org.biojava.bio.taxa.EbiFormat
- All Implemented Interfaces:
TaxonParser
Deprecated.
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
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final EbiFormat
Deprecated.parse
(TaxonFactory taxonFactory, String taxonString) Deprecated.Convert a stringified Taxon into a Taxon instance.Deprecated.Convert a Taxon into a stringified representation.serializeSource
(Taxon taxon) Deprecated.serializeXRef
(Taxon taxon) Deprecated.
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Field Details
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PROPERTY_NCBI_TAXON
Deprecated. -
PROPERTY_TAXON_NAMES
Deprecated.
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Constructor Details
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EbiFormat
public EbiFormat()Deprecated.
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Method Details
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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 interfaceTaxonParser
- Parameters:
taxonFactory
- the TaxonFactory used to instantiate taxa instancestaxonString
- the String to parse- Returns:
- a Taxon instance created by the TaxonFactory from the taxonString
- Throws:
ChangeVetoException
CircularReferenceException
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serialize
Deprecated.Description copied from interface:TaxonParser
Convert a Taxon into a stringified representation.- Specified by:
serialize
in interfaceTaxonParser
- Parameters:
taxon
- the Taxon to serialize- Returns:
- the stringified version of Taxon
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serializeSource
Deprecated. -
serializeXRef
Deprecated.
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org.biojavax.bio.taxa