Uses of Interface org.biojava.bio.taxa.Taxon (BioJava-1.5-beta API)

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## 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.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.
`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, 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.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.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
`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
`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
`protected Taxon` | `WeakTaxon.parent` Deprecated.
`protected Taxon` | `SimpleTaxon.parent` Deprecated.

Methods in org.biojava.bio.taxa that return Taxon
`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.addChild(Taxon parent, Taxon child)` 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` | `SimpleTaxonFactory.createTaxon(String scientificName, String commonName)` Deprecated.
`Taxon` | `WeakTaxon.getParent()` Deprecated.
`Taxon` | `SimpleTaxon.getParent()` Deprecated.
`Taxon` | `Taxon.getParent()` Deprecated. The parent of this Taxon.
`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.getRoot()` 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.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` | `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.removeChild(Taxon parent, Taxon child)` Deprecated.
`Taxon` | `TaxonFactory.search(Object id)` Deprecated. Retrieve a Taxon that matches some ID.
`Taxon` | `WeakTaxonFactory.search(Object id)` Deprecated.
`Taxon` | `SimpleTaxonFactory.search(Object id)` Deprecated.

Methods in org.biojava.bio.taxa with parameters of type Taxon
`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.addChild(Taxon parent, Taxon child)` 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.importTaxon(Taxon taxon)` 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.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.

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