Uses of Class
org.biojava.bio.seq.db.biosql.DBHelper

Packages that use DBHelper

Package	Description
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.

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

Subclasses of DBHelper in org.biojava.bio.seq.db.biosql

Modifier and Type	Class	Description
class	HypersonicDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db
class	MySQLDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db
class	OracleDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db
class	PostgreSQLDBHelper
class	UnknownDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db

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

Modifier and Type	Method	Description
static DBHelper	DBHelper.getDBHelper(Connection conn)	Deprecated. Returns a DBHelper implementation suitable for a particular database.

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

Modifier and Type	Method	Description
static void	TaxonSQL.automaticUpdate(Connection conn, DBHelper helper, TaxonFactory factory, File delnodes, File merged)	Deprecated. This method tries to perform a complete update according to the given TaxonFactory, which already contains the newes taxa and the files available at the NCBI-FTP-Site.
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.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.