Uses of Interface
org.biojava.bio.taxa.Taxon
Packages that use Taxon
Package
Description
General purpose Sequence storage in a relational database.
Taxonomy object for representing species information.
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Uses of Taxon in org.biojava.bio.seq.db.biosql
Methods in org.biojava.bio.seq.db.biosql that return TaxonModifier and TypeMethodDescriptionstatic Taxon
TaxonSQL.addName
(Connection conn, Taxon taxon, String nameClass, String newName) Deprecated.Adds a new name of the givennameClass
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 TaxonModifier and TypeMethodDescriptionstatic Taxon
TaxonSQL.addName
(Connection conn, Taxon taxon, String nameClass, String newName) Deprecated.Adds a new name of the givennameClass
to the taxon.static Stack
TaxonSQL.getChildrenOf
(Connection conn, Taxon t) Deprecated.Returns the children as aStack
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 aTaxon
(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 specifiedString
.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 TaxonModifier and TypeClassDescriptionclass
Deprecated.class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
Fields in org.biojava.bio.taxa declared as TaxonModifier and TypeFieldDescriptionprotected Taxon
SimpleTaxon.parent
Deprecated.protected Taxon
WeakTaxon.parent
Deprecated.Methods in org.biojava.bio.taxa that return TaxonModifier and TypeMethodDescriptionDeprecated.Deprecated.Add a taxon as a child to a parent.Deprecated.SimpleTaxonFactory.createTaxon
(String scientificName, String commonName) Deprecated.TaxonFactory.createTaxon
(String scientificName, String commonName) Deprecated.Create a new orphan Taxon with a given scientific and common name.WeakTaxonFactory.createTaxon
(String scientificName, String commonName) Deprecated.SimpleTaxon.getParent()
Deprecated.Taxon.getParent()
Deprecated.The parent of this Taxon.WeakTaxon.getParent()
Deprecated.SimpleTaxonFactory.getRoot()
Deprecated.TaxonFactory.getRoot()
Deprecated.Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.WeakTaxonFactory.getRoot()
Deprecated.SimpleTaxonFactory.importTaxon
(Taxon taxon) Deprecated.TaxonFactory.importTaxon
(Taxon source) Deprecated.Import a Taxon and all its children into the implementation provided by this factory.WeakTaxonFactory.importTaxon
(Taxon taxon) Deprecated.EbiFormat.parse
(TaxonFactory taxonFactory, String taxonString) Deprecated.TaxonParser.parse
(TaxonFactory taxonFactory, String taxonString) Deprecated.Convert a stringified Taxon into a Taxon instance.SimpleTaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.TaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.Remove a Taxon as a child to this one.WeakTaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.Deprecated.Deprecated.Retrieve a Taxon that matches some ID.Deprecated.Methods in org.biojava.bio.taxa with parameters of type TaxonModifier and TypeMethodDescriptionDeprecated.Deprecated.Add a taxon as a child to a parent.Deprecated.SimpleTaxonFactory.importTaxon
(Taxon taxon) Deprecated.TaxonFactory.importTaxon
(Taxon source) Deprecated.Import a Taxon and all its children into the implementation provided by this factory.WeakTaxonFactory.importTaxon
(Taxon taxon) Deprecated.SimpleTaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.TaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.Remove a Taxon as a child to this one.WeakTaxonFactory.removeChild
(Taxon parent, Taxon child) Deprecated.Deprecated.Deprecated.Convert a Taxon into a stringified representation.EbiFormat.serializeSource
(Taxon taxon) Deprecated.EbiFormat.serializeXRef
(Taxon taxon) Deprecated.
org.biojavax.bio.taxa