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:

Changeable, SequenceDB, SequenceDBLite, java.io.Serializable

public class SubSequenceDB

extends SequenceDBWrapper

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested classes 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

SubSequenceDB(SequenceDB parent, java.util.Set ids)

Method Summary

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, 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,
                     java.util.Set ids)
              throws BioException

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.

Returns:

the Sequence with that id

Throws:

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