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(java.sql.Connection conn, Taxon taxon, java.lang.String nameClass, java.lang.String newName)
          Deprecated. Adds a new name of the given nameClass to the taxon.
static Taxon TaxonSQL.getDBTaxon(java.sql.Connection conn, int taxon_id)
          Deprecated. Attempts to get a Taxon object corresponding to the specified taxon_id (i.e.
static Taxon TaxonSQL.getTaxon(java.sql.Connection conn, int ncbi_taxon_id)
          Deprecated. Attempts to get a Taxon object corresponding to the specified NCBI taxon ID.
static Taxon TaxonSQL.getTaxon(java.sql.Connection conn, java.lang.String name)
          Deprecated. Attempts to get a Taxon object corresponding to the specified name.
static Taxon TaxonSQL.removeName(java.sql.Connection conn, DBHelper helper, Taxon taxon, java.lang.String nameClass, java.lang.String oldName)
          Deprecated. Deletes the specified name from of the taxon from the database.
static Taxon TaxonSQL.removeTaxon(java.sql.Connection conn, DBHelper helper, java.lang.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(java.sql.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(java.sql.Connection conn, Taxon taxon, java.lang.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(java.sql.Connection conn, Taxon taxon, java.lang.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(java.sql.Connection conn, Taxon taxon, java.lang.String nameClass, java.lang.String newName)
          Deprecated. Adds a new name of the given nameClass to the taxon.
static java.util.Stack TaxonSQL.getChildrenOf(java.sql.Connection conn, Taxon t)
          Deprecated. Returns the children as a Stack of this given taxon.
static java.lang.String TaxonSQL.getRealScientificName(Taxon t)
          Deprecated. This returns the true scientific name of a given taxon, if there is one.
static int TaxonSQL.putTaxon(java.sql.Connection conn, DBHelper helper, Taxon taxon)
          Deprecated. Adds a Taxon (along with its parents) to the database.
static void TaxonSQL.removeGeneticCodeID(java.sql.Connection conn, DBHelper helper, Taxon tdb)
          Deprecated. Deletes the genetic code annotation from the taxon in the database.
static void TaxonSQL.removeLeftValue(java.sql.Connection conn, DBHelper helper, Taxon tdb)
          Deprecated. Deletes the left value from the specified taxon in the database.
static void TaxonSQL.removeMitochondrialGeneticCodeID(java.sql.Connection conn, DBHelper helper, Taxon tdb)
          Deprecated. Deletes the so called mitochondrial genetic code annotation from the given taxon.
static Taxon TaxonSQL.removeName(java.sql.Connection conn, DBHelper helper, Taxon taxon, java.lang.String nameClass, java.lang.String oldName)
          Deprecated. Deletes the specified name from of the taxon from the database.
static void TaxonSQL.removeRank(java.sql.Connection conn, DBHelper helper, Taxon tdb)
          Deprecated. Removes the rank persistently from the taxon in the database.
static void TaxonSQL.removeRightValue(java.sql.Connection conn, DBHelper helper, Taxon tdb)
          Deprecated. Deletes the right value from the specified taxon in the database.
static Taxon TaxonSQL.setCommonName(java.sql.Connection conn, Taxon taxon, java.lang.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(java.sql.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(java.sql.Connection conn, Taxon tdb, int left)
          Deprecated. Updates the taxon and sets the left value to the specified value.
static void TaxonSQL.setMitochondrialGeneticCodeID(java.sql.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(java.sql.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(java.sql.Connection conn, Taxon tdb, java.lang.String rank)
          Deprecated. Updates a taxon and sets it's rank to the specified String.
static void TaxonSQL.setRightValue(java.sql.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(java.sql.Connection conn, Taxon taxon, java.lang.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 SimpleTaxon.parent
          Deprecated.  
protected  Taxon WeakTaxon.parent
          Deprecated.  
 

Methods in org.biojava.bio.taxa that return Taxon
 Taxon WeakTaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon TaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated. Add a taxon as a child to a parent.
 Taxon SimpleTaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon WeakTaxonFactory.createTaxon(java.lang.String scientificName, java.lang.String commonName)
          Deprecated.  
 Taxon TaxonFactory.createTaxon(java.lang.String scientificName, java.lang.String commonName)
          Deprecated. Create a new orphan Taxon with a given scientific and common name.
 Taxon SimpleTaxonFactory.createTaxon(java.lang.String scientificName, java.lang.String commonName)
          Deprecated.  
 Taxon SimpleTaxon.getParent()
          Deprecated.  
 Taxon WeakTaxon.getParent()
          Deprecated.  
 Taxon Taxon.getParent()
          Deprecated. The parent of this Taxon.
 Taxon WeakTaxonFactory.getRoot()
          Deprecated.  
 Taxon TaxonFactory.getRoot()
          Deprecated. Retrieve the root upon which all rooted Taxon that this factory knows about are rooted.
 Taxon SimpleTaxonFactory.getRoot()
          Deprecated.  
 Taxon WeakTaxonFactory.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 SimpleTaxonFactory.importTaxon(Taxon taxon)
          Deprecated.  
 Taxon EbiFormat.parse(TaxonFactory taxonFactory, java.lang.String taxonString)
          Deprecated.  
 Taxon TaxonParser.parse(TaxonFactory taxonFactory, java.lang.String taxonString)
          Deprecated. Convert a stringified Taxon into a Taxon instance.
 Taxon WeakTaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon TaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated. Remove a Taxon as a child to this one.
 Taxon SimpleTaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon WeakTaxonFactory.search(java.lang.Object id)
          Deprecated.  
 Taxon TaxonFactory.search(java.lang.Object id)
          Deprecated. Retrieve a Taxon that matches some ID.
 Taxon SimpleTaxonFactory.search(java.lang.Object id)
          Deprecated.  
 

Methods in org.biojava.bio.taxa with parameters of type Taxon
 Taxon WeakTaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon TaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated. Add a taxon as a child to a parent.
 Taxon SimpleTaxonFactory.addChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon WeakTaxonFactory.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 SimpleTaxonFactory.importTaxon(Taxon taxon)
          Deprecated.  
 Taxon WeakTaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated.  
 Taxon TaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated. Remove a Taxon as a child to this one.
 Taxon SimpleTaxonFactory.removeChild(Taxon parent, Taxon child)
          Deprecated.  
 java.lang.String EbiFormat.serialize(Taxon taxon)
          Deprecated.  
 java.lang.String TaxonParser.serialize(Taxon taxon)
          Deprecated. Convert a Taxon into a stringified representation.
 java.lang.String EbiFormat.serializeSource(Taxon taxon)
          Deprecated.  
 java.lang.String EbiFormat.serializeXRef(Taxon taxon)
          Deprecated.