Package org.biojava.bio.seq.db

Class DummySequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

org.biojava.bio.seq.db.DummySequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable

public class DummySequenceDB
extends AbstractSequenceDB
implements SequenceDB

DummySequenceDB is an implementation which contains only a DummySequence. It will return the same DummySequence instance regardless of the sequence id used to retrieve a sequence.

Since:

1.2

Author:

Keith James

Field Summary

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
DummySequenceDB(String name)

Method Summary

Modifier and Type	Method	Description
void	addSequence(Sequence seq)	Adds a sequence to the database.
String	getName()	Get the name of this sequence database.
Sequence	getSequence(String id)	Retrieve a single sequence by its id.
Set	ids()	Get an immutable set of all of the IDs in the database.
void	removeSequence(String id)	Remove the sequence associated with an ID from the database.
SequenceIterator	sequenceIterator()	Returns a SequenceIterator over all sequences in the database.

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB

filter

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.db.SequenceDB

filter

Constructor Detail

DummySequenceDB

public DummySequenceDB(String name)

Method Detail

ids

public Set ids()

Description copied from interface: SequenceDB

Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

Specified by:

ids in interface SequenceDB

Returns:

a Set of ids - at the moment, strings

sequenceIterator

public SequenceIterator sequenceIterator()

Description copied from interface: SequenceDB

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.

Specified by:

sequenceIterator in interface SequenceDB

Overrides:

sequenceIterator in class AbstractSequenceDB

Returns:

a SequenceIterator over all sequences

getName

public String getName()

Description copied from interface: SequenceDBLite

Get the name of this sequence database.

Specified by:

getName in interface SequenceDBLite

Returns:

the name of the sequence database, which may be null.

getSequence

public Sequence getSequence(String id)
                     throws IllegalIDException,
                            BioException

Description copied from interface: SequenceDBLite

Retrieve a single sequence by its id.

Specified by:

getSequence in interface SequenceDBLite

Parameters:

id - the id to retrieve by

Returns:

the Sequence with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException - if there was a failure in retrieving the sequence

addSequence

public void addSequence(Sequence seq)
                 throws IllegalIDException,
                        BioException,
                        ChangeVetoException

Description copied from interface: SequenceDBLite

Adds a sequence to the database.

Specified by:

addSequence in interface SequenceDBLite

Overrides:

addSequence in class AbstractSequenceDB

Parameters:

seq - the Sequence to add

Throws:

IllegalIDException - if a uniqe ID could not be generated for seq

BioException - if something goes wrong with adding the sequence

ChangeVetoException - if either the database does not allow sequences to be added or the modification was vetoed

removeSequence

public void removeSequence(String id)
                    throws IllegalIDException,
                           BioException,
                           ChangeVetoException

Description copied from interface: SequenceDBLite

Remove the sequence associated with an ID from the database.

Specified by:

removeSequence in interface SequenceDBLite

Overrides:

removeSequence in class AbstractSequenceDB

Parameters:

id - the ID of the sequence to remove

Throws:

IllegalIDException - if there is no sequence for the ID

BioException - if something failed while removing the sequence for that ID

ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed