Package org.biojava.bio

Interface Annotatable

All Superinterfaces:

Changeable

All Known Subinterfaces:

Alphabet, AtomicSymbol, BasisSymbol, BioEntry, ComparableTerm, ComparableTriple, ComponentFeature, CrossRef, DotState, EmissionState, Feature, FeatureTypes.Repository, FeatureTypes.Type, FiniteAlphabet, FramedFeature, GappedSequence, GFF3Record, HomologyFeature, ModelInState, OntologyTerm, RemoteFeature, RemoteTerm, RestrictionSite, RichAnnotatable, RichFeature, RichLocation, RichSequence, SeqSimilaritySearchHit, SeqSimilaritySearchResult, SeqSimilaritySearchSubHit, Sequence, SimilarityPairFeature, State, StrandedFeature, Symbol, SymbolTokenization, Taxon, Term, Triple, UnigeneCluster, Variable

All Known Implementing Classes:

AbstractAlphabet, AbstractSymbol, AbstractTaxon, AbstractTerm, AlternateTokenization, CharacterTokenization, CircularView, CompoundRichLocation, CrossProductTokenization, DoubleAlphabet, DoubleAlphabet.DoubleRange, DoubleAlphabet.DoubleSymbol, DoubleAlphabet.SubDoubleAlphabet, DoubleTokenization, DummySequence, EmptyRichLocation, FeatureTypes.RepositoryImpl, FundamentalAtomicSymbol, GFF3Record.Impl, IntegerAlphabet, IntegerAlphabet.IntegerSymbol, IntegerAlphabet.SubIntegerAlphabet, IntegerOntology.IntTerm, IntegerTokenization, MagicalState, MultiSourceCompoundRichLocation, NameTokenization, NewSimpleAssembly, OntologyTerm.Impl, PhredSequence, ProfileEmissionState, ProjectedFeature, RemoteTerm.Impl, RevCompSequence, SequenceDBSearchHit, SequenceDBSearchResult, SequenceDBSearchSubHit, SimpleAlphabet, SimpleAssembly, SimpleAtomicSymbol, SimpleBioEntry, SimpleComparableTerm, SimpleComparableTriple, SimpleCrossRef, SimpleDotState, SimpleEmissionState, SimpleFeature, SimpleFramedFeature, SimpleGappedSequence, SimpleHomologyFeature, SimpleModelInState, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleRichLocation, SimpleRichSequence, SimpleSeqSimilaritySearchHit, SimpleSeqSimilaritySearchResult, SimpleSeqSimilaritySearchSubHit, SimpleSequence, SimpleSimilarityPairFeature, SimpleStrandedFeature, SimpleTaxon, SingletonAlphabet, SoftMaskedAlphabet, SoftMaskedAlphabet.CaseSensitiveTokenization, SubIntegerTokenization, SubSequence, Term.Impl, ThinRichSequence, Triple.Impl, Variable.Impl, ViewSequence, WeakTaxon, WordTokenization

public interface Annotatable
extends Changeable

Indicates that an object has an associated annotation.

Many BioJava objects will have associated unstructured data. This should be stored in an Annotation instance. However, the BioJava object itself will probably not want to extend the Annotation interface directly, but rather delegate off that functionality to an Annotation property. The Annotatable interface indicates that there is an Annotation property. When implementing Annotatable, you should always create a protected or private field containing an instance of ChangeForwarder, and register it as a ChangeListener with the associated Annotation delegate instance.

 public class Foo extends AbstractChangeable implements Annotatable {
   private Annotation ann; // the associated annotation delegate
   protected ChangeForwarder annFor; // the event forwarder

   public Foo() {
     // make the ann delegate
     ann = new SimpleAnnotation();
     // construct the forwarder so that it emits Annotatable.ANNOTATION ChangeEvents
     // for the Annotation.PROPERTY events it will listen for
     annFor = new ChangeForwarder.Retyper(this, getChangesupport( Annotatable.ANNOTATION ), 
                                          Annotatable.ANNOTATION );
     // connect the forwarder so it listens for Annotation.PROPERTY events
     ann.addChangeListener( annFor, Annotation.PROPERTY ); 
   }

   public Annotation getAnnotation() {
     return ann;
   }
 }
 

Check if BioJava classes and interfaces extend Annotatable. This will tell you if you should look for associated annotation. If an object implements Annotatable, it may well propagate ChangeEvent notifications from the associated Annotation. You may need to track these to maintain the state of your applications. Be careful to hook up the appropriate event forwarders. The getAnnotation() method can be implemented lazily (instantiate the Annotation instance and event forwarders when the first request comes in). It can also be implemented by returning throw-away immutable Annotation instances that are built from scratch each time.

Since:

1.0

Author:

Matthew Pocock, Keith James (docs)., Kalle N�slund (docs)

See Also:

RichAnnotatable

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	Annotatable.AnnotationForwarder	Deprecated. use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	ANNOTATION	Signals that the associated Annotation has altered in some way.

Method Summary

Modifier and Type	Method	Description
Annotation	getAnnotation()	Should return the associated annotation object.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

ANNOTATION

static final ChangeType ANNOTATION

Signals that the associated Annotation has altered in some way. The chainedEvent property should refer back to the event fired by the Annotation object.

Method Detail

getAnnotation

Annotation getAnnotation()

Should return the associated annotation object.

Returns:

an Annotation object, never null