org.biojava.bio
Interface Annotatable

All Superinterfaces:

Changeable

All Known Subinterfaces:

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

All Known Implementing Classes:

AbstractAlphabet, org.biojava.bio.symbol.AbstractSimpleBasisSymbol, AbstractSymbol, AbstractTaxon, AbstractTerm, CharacterTokenization, DoubleAlphabet, DoubleAlphabet.DoubleRange, DoubleAlphabet.DoubleSymbol, DoubleAlphabet.SubDoubleAlphabet, DummySequence, FeatureTypes.RepositoryImpl, FundamentalAtomicSymbol, GFF3Record.Impl, IntegerAlphabet, IntegerAlphabet.IntegerSymbol, IntegerOntology.IntTerm, NewSimpleAssembly, OntologyTerm.Impl, ProjectedFeature, RemoteTerm.Impl, SequenceDBSearchHit, SequenceDBSearchResult, SequenceDBSearchSubHit, SimpleAssembly, SimpleAtomicSymbol, SimpleDotState, SimpleEmissionState, SimpleFeature, SimpleFramedFeature, SimpleGappedSequence, SimpleHomologyFeature, SimpleModelInState, SimpleRemoteFeature, SimpleRestrictionSite, SimpleSeqSimilaritySearchHit, SimpleSeqSimilaritySearchResult, SimpleSeqSimilaritySearchSubHit, SimpleSequence, SimpleSimilarityPairFeature, SimpleStrandedFeature, org.biojava.bio.symbol.SimpleSymbol, SingletonAlphabet, SoftMaskedAlphabet, SoftMaskedAlphabet.CaseSensitiveTokenization, SubSequence, Term.Impl, Triple.Impl, Variable.Impl, ViewSequence, 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;
   }
 }
 

Since:

1.0

Author:

Matthew Pocock, Keith James (docs)., Kalle Näslund (docs)

For general use:

Check if BioJava classes and interfaces extend Annotatable. This will tell you if you should look for associated annotation.

For advanced users:

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.

For developers:

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.

Nested Class Summary

static class

Annotatable.AnnotationForwarder Deprecated. use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead

Field Summary

static ChangeType

ANNOTATION Signals that the associated Annotation has altered in some way.

Method Summary

Annotation

getAnnotation() Should return the associated annotation object.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

ANNOTATION

public 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

public Annotation getAnnotation()

Should return the associated annotation object.

Returns:

an Annotation object, never null