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

Packages that use DBHelper
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
 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
static DBHelper DBHelper.getDBHelper(java.sql.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
static void TaxonSQL.automaticUpdate(java.sql.Connection conn, DBHelper helper, TaxonFactory factory, java.io.File delnodes, java.io.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(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.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.