Package org.biojava.bio.seq.db

Class DummySequenceDBInstallation

java.lang.Object

org.biojava.bio.seq.db.DummySequenceDBInstallation

All Implemented Interfaces:

SequenceDBInstallation

public class DummySequenceDBInstallation
extends Object
implements SequenceDBInstallation

DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.

Since:

1.2

Author:

Keith James

Constructor Summary

Constructors

Constructor	Description
DummySequenceDBInstallation()

Method Summary

Modifier and Type	Method	Description
void	addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers)	As this is a dummy implementation adding a sequenceDB doesn't do anything
SequenceDBLite	getSequenceDB(String identifier)	Return the SequenceDB for the given identifier.
Set	getSequenceDBs()	Return all sequence dbs available in this sequence db installation.

Methods inherited from class java.lang.Object

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

Constructor Detail

DummySequenceDBInstallation

public DummySequenceDBInstallation()

Method Detail

getSequenceDB

public SequenceDBLite getSequenceDB(String identifier)

Description copied from interface: SequenceDBInstallation

Return the SequenceDB for the given identifier. The identifier can (but need not) be the name of the sequence db. An implementation may support any number of identifiers to (uniquely) identify a particular sequence db - but the name of the sequence db (returned by SequenceDB.getName()) must always be among them.

If the sequence db identified by the given identifier has not been requested through this object, it will be created and returned (hence this method is a factory method). If the sequence db identified by the given identifier has already been requested, the same object is returned.

Specified by:

getSequenceDB in interface SequenceDBInstallation

Parameters:

identifier - the string that identifies the sequence db. May not be null.

Returns:

the SequenceDB object that matches the given identifier or null if no such SequenceDB object could be found. (It is the responsibility of the implementation to take care that all identifiers are unique so if it turns out that the given identifier identifies more than one sequence db, this method should throw a RuntimeException.)

getSequenceDBs

public Set getSequenceDBs()

Description copied from interface: SequenceDBInstallation

Return all sequence dbs available in this sequence db installation. This is not just the set of sequence dbs already returned by getSequenceDB() but the entire set of sequence dbs supported by this object.

Specified by:

getSequenceDBs in interface SequenceDBInstallation

Returns:

a set of SequenceDB objects which may be empty. An implementation may also return null if it is not at all possible to determine which sequence dbs are part of this installation.

addSequenceDB

public void addSequenceDB(SequenceDBLite sequenceDB,
                          Set otherIdentifiers)

As this is a dummy implementation adding a sequenceDB doesn't do anything

Specified by:

addSequenceDB in interface SequenceDBInstallation

Parameters:

sequenceDB - a SequenceDB.

otherIdentifiers - a Set.