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

Packages that use Taxon

Package	Description
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

Modifier and Type	Method	Description
static Taxon	TaxonSQL.addName(Connection conn, Taxon taxon, String nameClass, String newName)	Deprecated. Adds a new name of the given nameClass to the taxon.
static Taxon	TaxonSQL.getDBTaxon(Connection conn, int taxon_id)	Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e. the database's internal id for the taxon).
static Taxon	TaxonSQL.getTaxon(Connection conn, int ncbi_taxon_id)	Deprecated. Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.
static Taxon	TaxonSQL.getTaxon(Connection conn, String name)	Deprecated. Attempts to get a Taxon object corresponding to the specified name.
static Taxon	TaxonSQL.removeName(Connection conn, DBHelper helper, Taxon taxon, String nameClass, String oldName)	Deprecated. Deletes the specified name from of the taxon from the database.
static Taxon	TaxonSQL.removeTaxon(Connection conn, int ncbi_id, DBHelper helper)	Deprecated. Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the removed taxon.
static Taxon	TaxonSQL.removeTaxon(Connection conn, DBHelper helper, String name)	Deprecated. Deletes a taxon specified by one of it's names with all it's different names, annotations and sequences from the database.
static Taxon	TaxonSQL.setCommonName(Connection conn, Taxon taxon, String newName)	Deprecated. With this method the common name of the given taxon can be changed or created, if there was none before.
static Taxon	TaxonSQL.setScientificName(Connection conn, Taxon taxon, String newName)	Deprecated. This changes the scientific name of the given taxon and stores the new name persistent in the database.

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

Modifier and Type	Method	Description
static Taxon	TaxonSQL.addName(Connection conn, Taxon taxon, String nameClass, String newName)	Deprecated. Adds a new name of the given nameClass to the taxon.
static Stack	TaxonSQL.getChildrenOf(Connection conn, Taxon t)	Deprecated. Returns the children as a Stack of this given taxon.
static String	TaxonSQL.getRealScientificName(Taxon t)	Deprecated. This returns the true scientific name of a given taxon, if there is one.
static int	TaxonSQL.putTaxon(Connection conn, DBHelper helper, Taxon taxon)	Deprecated. Adds a Taxon (along with its parents) to the database.
static void	TaxonSQL.removeGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb)	Deprecated. Deletes the genetic code annotation from the taxon in the database.
static void	TaxonSQL.removeLeftValue(Connection conn, DBHelper helper, Taxon tdb)	Deprecated. Deletes the left value from the specified taxon in the database.
static void	TaxonSQL.removeMitochondrialGeneticCodeID(Connection conn, DBHelper helper, Taxon tdb)	Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon.
static Taxon	TaxonSQL.removeName(Connection conn, DBHelper helper, Taxon taxon, String nameClass, String oldName)	Deprecated. Deletes the specified name from of the taxon from the database.
static void	TaxonSQL.removeRank(Connection conn, DBHelper helper, Taxon tdb)	Deprecated. Removes the rank persistently from the taxon in the database.
static void	TaxonSQL.removeRightValue(Connection conn, DBHelper helper, Taxon tdb)	Deprecated. Deletes the right value from the specified taxon in the database.
static Taxon	TaxonSQL.setCommonName(Connection conn, Taxon taxon, String newName)	Deprecated. With this method the common name of the given taxon can be changed or created, if there was none before.
static void	TaxonSQL.setGeneticCodeID(Connection conn, Taxon tdb, int id)	Deprecated. Updates the taxon in the database and sets its genetic code id to the specified value.
static void	TaxonSQL.setLeftValue(Connection conn, Taxon tdb, int left)	Deprecated. Updates the taxon and sets the left value to the specified value.
static void	TaxonSQL.setMitochondrialGeneticCodeID(Connection conn, Taxon tdb, int id)	Deprecated. Updates the given taxon and sets it's so called mitochondrial genetic code id to the specified value.
static void	TaxonSQL.setParent(Connection conn, Taxon child, Taxon parent)	Deprecated. This updates the taxonomic tree in the database and sets the parent of the given child taxon to the parent taxon.
static void	TaxonSQL.setRank(Connection conn, Taxon tdb, String rank)	Deprecated. Updates a taxon and sets it's rank to the specified String.
static void	TaxonSQL.setRightValue(Connection conn, Taxon tdb, int right)	Deprecated. Updates the taxon in the database and sets the right value to the specified value.
static Taxon	TaxonSQL.setScientificName(Connection conn, Taxon taxon, String newName)	Deprecated. This changes the scientific name of the given taxon and stores the new name persistent in the database.

Uses of Taxon in org.biojava.bio.taxa

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

Modifier and Type	Class	Description
class	AbstractTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
class	SimpleTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
class	WeakTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa

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

Modifier and Type	Field	Description
protected Taxon	SimpleTaxon.parent	Deprecated.
protected Taxon	WeakTaxon.parent	Deprecated.

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

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

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

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