Uses of Class
org.biojava.bio.seq.db.biosql.DBHelper
Packages that use DBHelper
Package
Description
General purpose Sequence storage in a relational database.
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Uses of DBHelper in org.biojava.bio.seq.db.biosql
Subclasses of DBHelper in org.biojava.bio.seq.db.biosqlModifier and TypeClassDescriptionclass
Deprecated.Use hibernate and org.biojavax.bio.dbclass
Deprecated.Use hibernate and org.biojavax.bio.dbclass
Deprecated.Use hibernate and org.biojavax.bio.dbclass
class
Deprecated.Use hibernate and org.biojavax.bio.dbMethods in org.biojava.bio.seq.db.biosql that return DBHelperModifier and TypeMethodDescriptionstatic 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 DBHelperModifier and TypeMethodDescriptionstatic 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 givenTaxonFactory
, 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 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.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.