Package org.bridgedb.rdb

Class SimpleGdb

java.lang.Object

org.bridgedb.rdb.IDMapperRdb

org.bridgedb.rdb.SimpleGdb

All Implemented Interfaces:

AttributeMapper, IDMapper, XrefIterator

Direct Known Subclasses:

SimpleGdbImplCommon

public abstract class SimpleGdb
extends IDMapperRdb

SimpleGdb is the main implementation of the Gdb interface, for dealing with single SQL-based pgdb's. It's responsible for creating and querying a single pgdb relational database through the JDBC interface.

It wraps SQL statements in methods, so the rest of the apps don't need to know the details of the Database schema.

It delegates dealing with the differences between various RDBMS's (Derby, Hsqldb etc.) to a DBConnector instance. A correct DBConnector instance needs to be passed to the constructor of SimpleGdb.

In the PathVisio GUI environment, use GdbManager to create and connect one or two centralized Gdb's. This will also automatically find the right DBConnector from the preferences.

In a head-less or test environment, you can bypass GdbManager and use SimpleGdb directly to create or connect to one or more pgdb's of any type.

Field Summary

Fields

Modifier and Type	Field	Description
protected String	dbName
static int	NO_LIMIT
static int	NO_TIMEOUT
static int	QUERY_TIMEOUT

Fields inherited from interface org.bridgedb.AttributeMapper

MATCH_ID

Method Summary

Modifier and Type	Method	Description
void	close()
Connection	getConnection()
String	getDbName()	Gets the name of te currently used gene database.
int	getGeneCount()
int	getGeneCount(DataSource ds)
int	getLinkCount()
boolean	isConnected()

Methods inherited from class org.bridgedb.rdb.IDMapperRdb

mapID, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.bridgedb.AttributeMapper

freeAttributeSearch, freeAttributeSearchEx, getAttributes, getAttributes, getAttributeSet, isFreeAttributeSearchSupported

Methods inherited from interface org.bridgedb.IDMapper

freeSearch, getCapabilities, mapID, xrefExists

Methods inherited from interface org.bridgedb.XrefIterator

getIterator, getIterator

Field Detail

dbName

protected final String dbName

NO_LIMIT

public static final int NO_LIMIT

See Also:

Constant Field Values

NO_TIMEOUT

public static final int NO_TIMEOUT

See Also:

Constant Field Values

QUERY_TIMEOUT

public static final int QUERY_TIMEOUT

See Also:

Constant Field Values

Method Detail

getConnection

public Connection getConnection()
                         throws SQLException

Throws:

SQLException

isConnected

public final boolean isConnected()

getDbName

public final String getDbName()

Gets the name of te currently used gene database.

Specified by:

getDbName in class IDMapperRdb

Returns:

the database name as specified in the connection string

close

public final void close()
                 throws IDMapperException

Throws:

IDMapperException

getGeneCount

public final int getGeneCount()
                       throws IDMapperException

Returns:

number of rows in gene table.

Throws:

IDMapperException - on failure

getLinkCount

public final int getLinkCount()
                       throws IDMapperException

Returns:

number of rows in link table.

Throws:

IDMapperException - on failure

getGeneCount

public final int getGeneCount(DataSource ds)
                       throws IDMapperException

Parameters:

ds - DataSource to count identifiers for.

Returns:

number of identifiers table for the given datasource

Throws:

IDMapperException - on failure