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Packages that use DBHelper | |
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org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
Uses of DBHelper in org.biojava.bio.seq.db.biosql |
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Subclasses of DBHelper in org.biojava.bio.seq.db.biosql | |
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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
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class |
UnknownDBHelper
Deprecated. Use hibernate and org.biojavax.bio.db.* |
Methods in org.biojava.bio.seq.db.biosql that return DBHelper | |
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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 | |
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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. |
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