Package org.biojava.bio.seq.db

Class SubSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

org.biojava.bio.seq.db.SequenceDBWrapper

org.biojava.bio.seq.db.SubSequenceDB

All Implemented Interfaces:

Serializable, SequenceDB, SequenceDBLite, Changeable

public class SubSequenceDB
extends SequenceDBWrapper

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.seq.db.SequenceDBWrapper

SequenceDBWrapper.SequencesForwarder

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
SubSequenceDB(SequenceDB parent, Set ids)

Method Summary

Modifier and Type	Method	Description
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.

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

getChangeSupport, getParent

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

addSequence, filter, removeSequence, sequenceIterator

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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

Constructor Detail

SubSequenceDB

public SubSequenceDB(SequenceDB parent,
                     Set ids)
              throws BioException

Throws:

BioException

Method Detail

getName

public String getName()

Description copied from interface: SequenceDBLite

Get the name of this sequence database.

Returns:

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

getSequence

public Sequence getSequence(String id)
                     throws BioException

Description copied from interface: SequenceDBLite

Retrieve a single sequence by its id.

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

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.

Returns:

a Set of ids - at the moment, strings