Uses of Interface
org.biojava.bio.taxa.Taxon

Packages that use Taxon

org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.taxa	Taxonomy object for representing species information.

Uses of Taxon in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that return Taxon

static Taxon

TaxonSQL.getTaxon(Connection conn, int ncbi_taxon_id) Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.

Methods in org.biojava.bio.seq.db.biosql with parameters of type Taxon

static int

TaxonSQL.putTaxon(Connection conn, DBHelper helper, Taxon taxon) Adds a Taxon (along with its parents) to the database.

Uses of Taxon in org.biojava.bio.taxa

Classes in org.biojava.bio.taxa that implement Taxon

class	AbstractTaxon An abstract implementation of Taxon.
class	SimpleTaxon A no-frills implementatation of Taxon.
class	WeakTaxon An implementation of Taxon that keeps only weak references to children, but full references to parents.

Fields in org.biojava.bio.taxa declared as Taxon

protected Taxon	WeakTaxon.parent
protected Taxon	SimpleTaxon.parent

Methods in org.biojava.bio.taxa that return Taxon

Taxon	WeakTaxonFactory.getRoot()
Taxon	WeakTaxonFactory.importTaxon(Taxon taxon)
Taxon	WeakTaxonFactory.createTaxon(String scientificName, String commonName)
Taxon	WeakTaxonFactory.addChild(Taxon parent, Taxon child)
Taxon	WeakTaxonFactory.removeChild(Taxon parent, Taxon child)
Taxon	WeakTaxonFactory.search(Object id)
Taxon	WeakTaxon.getParent()
Taxon	TaxonParser.parse(TaxonFactory taxonFactory, String taxonString) Convert a stringified Taxon into a Taxon instance.
Taxon	TaxonFactory.importTaxon(Taxon source) Import a Taxon and all its children into the implementation provided by this factory.
Taxon	TaxonFactory.getRoot() Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
Taxon	TaxonFactory.search(Object id) Retrieve a Taxon that matches some ID.
Taxon	TaxonFactory.createTaxon(String scientificName, String commonName) Create a new orphan Taxon with a given scientific and common name.
Taxon	TaxonFactory.addChild(Taxon parent, Taxon child) Add a taxon as a child to a parent.
Taxon	TaxonFactory.removeChild(Taxon parent, Taxon child) Remove a Taxon as a child to this one.
Taxon	Taxon.getParent() The parent of this Taxon.
Taxon	SimpleTaxonFactory.getRoot()
Taxon	SimpleTaxonFactory.importTaxon(Taxon taxon)
Taxon	SimpleTaxonFactory.createTaxon(String scientificName, String commonName)
Taxon	SimpleTaxonFactory.addChild(Taxon parent, Taxon child)
Taxon	SimpleTaxonFactory.removeChild(Taxon parent, Taxon child)
Taxon	SimpleTaxonFactory.search(Object id)
Taxon	SimpleTaxon.getParent()
Taxon	EbiFormat.parse(TaxonFactory taxonFactory, String taxonString)

Methods in org.biojava.bio.taxa with parameters of type Taxon

Taxon	WeakTaxonFactory.importTaxon(Taxon taxon)
Taxon	WeakTaxonFactory.addChild(Taxon parent, Taxon child)
Taxon	WeakTaxonFactory.removeChild(Taxon parent, Taxon child)
String	TaxonParser.serialize(Taxon taxon) Convert a Taxon into a stringified representation.
Taxon	TaxonFactory.importTaxon(Taxon source) Import a Taxon and all its children into the implementation provided by this factory.
Taxon	TaxonFactory.addChild(Taxon parent, Taxon child) Add a taxon as a child to a parent.
Taxon	TaxonFactory.removeChild(Taxon parent, Taxon child) Remove a Taxon as a child to this one.
Taxon	SimpleTaxonFactory.importTaxon(Taxon taxon)
Taxon	SimpleTaxonFactory.addChild(Taxon parent, Taxon child)
Taxon	SimpleTaxonFactory.removeChild(Taxon parent, Taxon child)
String	EbiFormat.serialize(Taxon taxon)
String	EbiFormat.serializeSource(Taxon taxon)
String	EbiFormat.serializeXRef(Taxon taxon)