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

java.lang.Object
  extended by 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 java.lang.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(javax.sql.DataSource ds, java.lang.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(java.sql.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(java.sql.Connection conn, java.lang.String table, java.lang.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(java.sql.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(java.sql.Connection conn,
                                java.lang.String table,
                                java.lang.String columnName)
                         throws java.sql.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:
java.sql.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(javax.sql.DataSource ds,
                             java.lang.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:
java.lang.NullPointerException - if pool is null.
java.lang.IllegalArgumentException - if tablename is null or empty.