org.biojava.bio.seq.db.biosql

Class OracleDBHelper

java.lang.Object

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

org.biojava.bio.seq.db.biosql.OracleDBHelper

Deprecated.

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

public class OracleDBHelper
extends DBHelper

This is a DBHelper that provides support for Oracle databases.

Author:

Len Trigg, Eric Haugen, Richard Holland

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.seq.db.biosql.DBHelper

DBHelper.BioSequenceStyle, DBHelper.DeleteStyle, DBHelper.JoinStyle

Field Summary

Fields inherited from class org.biojava.bio.seq.db.biosql.DBHelper

BIOSEQUENCE_GENERIC, BIOSEQUENCE_ORACLECLOB, DELETE_GENERIC, DELETE_MYSQL4, DELETE_POSTGRESQL, JOIN_GENERIC, JOIN_ORACLE8

Constructor Summary

Constructors

Constructor and Description
OracleDBHelper(Connection connection) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
String	clobToString(Connection conn, ResultSet rs, int column) Deprecated.
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.
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.
void	stringToClob(Connection conn, ResultSet rs, int column, String value) Deprecated.

Methods inherited from class org.biojava.bio.seq.db.biosql.DBHelper

getDBHelper, getDeleteStyle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OracleDBHelper

public OracleDBHelper(Connection connection)

Deprecated.

Method Detail

getJoinStyle

public DBHelper.JoinStyle getJoinStyle()

Deprecated.

Description copied from class: DBHelper

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

Overrides:

getJoinStyle in class DBHelper

Returns:

the preferred joining style.

getInsertID

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

Deprecated.

Description copied from class: DBHelper

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

Specified by:

getInsertID in class DBHelper

Returns:

the last id assigned, or -1 if the id could not be found.

Throws:

SQLException

containsTable

public boolean containsTable(DataSource ds,
                    String tablename)

Deprecated.

Description copied from class: DBHelper

Detects whether a particular table is present in the database.

Overrides:

containsTable in class DBHelper

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.

getBioSequenceStyle

public DBHelper.BioSequenceStyle getBioSequenceStyle()

Deprecated.

Description copied from class: DBHelper

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.)

Overrides:

getBioSequenceStyle in class DBHelper

Returns:

the preferred joining style.

clobToString

public String clobToString(Connection conn,
                  ResultSet rs,
                  int column)

Deprecated.

stringToClob

public void stringToClob(Connection conn,
                ResultSet rs,
                int column,
                String value)

Deprecated.