Package org.biojava.bio.program.unigene

Interface UnigeneCluster

All Superinterfaces:

Annotatable, Changeable

public interface UnigeneCluster
extends Annotatable

A single unigene cluster.

This represents all of the information available about a single unigene cluster. This includes the sequences that are in it, the unique sequence that is its representative, the cluster id and all the annotation available via the data file. Much of the annotation may be accessible via the getAnnotation() method.

There is much more information in the Unigene clusters than just the id, title and sequences. This is all stoored in the annotation associated with the cluster. The annotation bundle conforms to the schema in UnigeneTools.UNIGENE_ANNOTATION.

Author:

Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method	Description
SequenceDB	getAll()	All sequences that map to this cluster.
String	getID()	The public unigene ID.
String	getTitle()	The cluster title.
Sequence	getUnique()	The unique sequence that is used as a representative for this cluster.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

getID

String getID()

The public unigene ID.

Returns:

get the cluster ID as a String

getTitle

String getTitle()

The cluster title.

Returns:

the cluster title as a String

getAll

SequenceDB getAll()

All sequences that map to this cluster.

Returns:

a SequenceDB of all sequences mapping to this cluster.

getUnique

Sequence getUnique()

The unique sequence that is used as a representative for this cluster.

Returns:

the cluster's unique Sequence