## org.biojava.bio.seq.db.biosql
Class DBHelper

    java.lang.Object
      org.biojava.bio.seq.db.biosql.DBHelper

Direct Known Subclasses:
  HypersonicDBHelper, MySQLDBHelper, OracleDBHelper, PostgreSQLDBHelper, UnknownDBHelper

Deprecated. Use hibernate and org.biojavax.bio.db.*

    public abstract class DBHelper

extends Object

Isolates all code that is specific to a particular RDBMS. To add support for a new RDBMS, write a new `DBHelper` subclass and ensure that it can be found by editing the `getDBHelperForURL` method in this class.

Author:
  Thomas Down, Matthew Pocock, Len Trigg, Eric Haugen, Richard Holland

Nested Class Summary
`static class` `DBHelper.BioSequenceStyle` Deprecated.
`static class` `DBHelper.DeleteStyle` Deprecated.
`static class` `DBHelper.JoinStyle` Deprecated.

Field Summary
`static DBHelper.BioSequenceStyle` `BIOSEQUENCE_GENERIC` Deprecated.
`static DBHelper.BioSequenceStyle` `BIOSEQUENCE_ORACLECLOB` Deprecated.
`static DBHelper.DeleteStyle` `DELETE_GENERIC` Deprecated.
`static DBHelper.DeleteStyle` `DELETE_MYSQL4` Deprecated.
`static DBHelper.DeleteStyle` `DELETE_POSTGRESQL` Deprecated.
`static DBHelper.JoinStyle` `JOIN_GENERIC` Deprecated.
`static DBHelper.JoinStyle` `JOIN_ORACLE8` Deprecated.

Constructor Summary
`DBHelper()` Deprecated.

Method Summary
`boolean` `containsTable(DataSource ds, String tablename)` Deprecated. Detects whether a particular table is present in the database.
`DBHelper.BioSequenceStyle` `getBioSequenceStyle()` Deprecated. Returns the an object indicating the style of biosequence storage that this database should employ.
`static DBHelper` `getDBHelper(Connection conn)` Deprecated. Returns a DBHelper implementation suitable for a particular database.
`DBHelper.DeleteStyle` `getDeleteStyle()` Deprecated. Returns the an object indicating the style of deletion that this database should employ.
`abstract int` `getInsertID(Connection conn, String table, String columnName)` Deprecated. Returns the id value created during the last insert command.
`DBHelper.JoinStyle` `getJoinStyle()` Deprecated. Returns the an object indicating the style of table joining that this database should employ.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### DELETE_POSTGRESQL

    public static final DBHelper.DeleteStyle DELETE_POSTGRESQL

  Deprecated.

### DELETE_MYSQL4

    public static final DBHelper.DeleteStyle DELETE_MYSQL4

  Deprecated.

### DELETE_GENERIC

    public static final DBHelper.DeleteStyle DELETE_GENERIC

  Deprecated.

### JOIN_ORACLE8

    public static final DBHelper.JoinStyle JOIN_ORACLE8

  Deprecated.

### JOIN_GENERIC

    public static final DBHelper.JoinStyle JOIN_GENERIC

  Deprecated.

### BIOSEQUENCE_GENERIC

    public static final DBHelper.BioSequenceStyle BIOSEQUENCE_GENERIC

  Deprecated.

### BIOSEQUENCE_ORACLECLOB

    public static final DBHelper.BioSequenceStyle BIOSEQUENCE_ORACLECLOB

  Deprecated.

Constructor Detail

### DBHelper

    public DBHelper()

  Deprecated.

Method Detail

### getDBHelper

    public static DBHelper getDBHelper(Connection conn)

  Deprecated.
  Returns a DBHelper implementation suitable for a particular database.

  Parameters:
    `conn` - a connection to the database.
  Returns:
    a `DBHelper`.

### getInsertID

    public abstract int getInsertID(Connection conn,
                                    String table,
                                    String columnName)
                             throws SQLException

  Deprecated.
  Returns the id value created during the last insert command. This is for tables that have an auto increment column.

  Returns:
    the last id assigned, or -1 if the id could not be found.
  Throws:
    `SQLException`

### getDeleteStyle

    public DBHelper.DeleteStyle getDeleteStyle()

  Deprecated.
  Returns the an object indicating the style of deletion that this database should employ. Unless overridden, this is DELETE_GENERIC.

  Returns:
    the preferred deletion style.

### getJoinStyle

    public DBHelper.JoinStyle getJoinStyle()

  Deprecated.
  Returns the an object indicating the style of table joining that this database should employ.

  Returns:
    the preferred joining style.

### getBioSequenceStyle

    public DBHelper.BioSequenceStyle getBioSequenceStyle()

  Deprecated.
  Returns the an object indicating the style of biosequence storage that this database should employ. Generally, leave it at the default unless you are using the Oracle schema, in which case you need to override it to return BIOSEQUENCE_ORACLECLOB. This is because, in the Oracle schema we need to use CLOBs (except when using Len Trigg's version which uses LONGs instead.)

  Returns:
    the preferred joining style.

### containsTable

    public boolean containsTable(DataSource ds,
                                 String tablename)

  Deprecated.
  Detects whether a particular table is present in the database.

  Parameters:
    `ds` - a `DataSource` that can provide a connection to a database
    `tablename` - the name of the table.
  Returns:
    true if the table exists in the database.
  Throws:
    `NullPointerException` - if pool is null.
    `IllegalArgumentException` - if tablename is null or empty.