org.biojava.bio.seq.db

Class ViewingSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

org.biojava.bio.seq.db.SequenceDBWrapper

org.biojava.bio.seq.db.ViewingSequenceDB

All Implemented Interfaces:

java.io.Serializable, SequenceDB, SequenceDBLite, Changeable

public class ViewingSequenceDB
extends SequenceDBWrapper

SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. One appropriate use of this would be to wrap a DB in one of these and then wrap this in an annotating db so that the annotation is added to views, not the underlying sequences.

Since:

1.2

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 and Description
ViewingSequenceDB(SequenceDB parent) Create a new ViewingSequenceDB that views the sequences in parent.

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getName() Get the name of this sequence database.
Sequence	getSequence(java.lang.String id) Retrieve a single sequence by its id.
java.util.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

ViewingSequenceDB

public ViewingSequenceDB(SequenceDB parent)

Create a new ViewingSequenceDB that views the sequences in parent.

Parameters:

parent - the SequenceDB to view

Method Detail

getName

public java.lang.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(java.lang.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 java.util.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