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

Nested Classes

Modifier and Type	Class and Description
static class	DBHelper.BioSequenceStyle Deprecated.
static class	DBHelper.DeleteStyle Deprecated.
static class	DBHelper.JoinStyle Deprecated.

Field Summary

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
DBHelper() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
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.