org.biojava.ontology

Class OntologyTerm.Impl

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.ontology.OntologyTerm.Impl

All Implemented Interfaces:

Serializable, Annotatable, OntologyTerm, Term, Changeable

Enclosing interface:

OntologyTerm

public static final class OntologyTerm.Impl
extends AbstractChangeable
implements OntologyTerm, Serializable

Simple in-memory implementation of a remote ontology term. This can be used to implement Ontology.importTerm

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.ontology.OntologyTerm

OntologyTerm.Impl

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

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.ontology.Term

ONTOLOGY

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
OntologyTerm.Impl(Ontology ontology, Ontology target)
OntologyTerm.Impl(Ontology ontology, Ontology target, Object[] synonyms)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSynonym(Object synonym) Add a synonym for this term.
Annotation	getAnnotation() Should return the associated annotation object.
ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object.
String	getDescription() Return a human-readable description of this term, or the empty string if none is available.
String	getName() Return the name of this term.
Ontology	getOntology() Get the remote ontology referenced by this term
Object[]	getSynonyms() Return the synonyms for this term.
Ontology	getTargetOntology()
void	removeSynonym(Object synonym) Remove a synonym for this term.
void	setDescription(String description) set the description of the term;
String	toString()

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, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

OntologyTerm.Impl

public OntologyTerm.Impl(Ontology ontology,
                 Ontology target)

OntologyTerm.Impl

public OntologyTerm.Impl(Ontology ontology,
                 Ontology target,
                 Object[] synonyms)

Method Detail

addSynonym

public void addSynonym(Object synonym)

Description copied from interface: Term

Add a synonym for this term.

Specified by:

addSynonym in interface Term

Parameters:

synonym - the synonym

removeSynonym

public void removeSynonym(Object synonym)

Description copied from interface: Term

Remove a synonym for this term.

Specified by:

removeSynonym in interface Term

getSynonyms

public Object[] getSynonyms()

Description copied from interface: Term

Return the synonyms for this term.

Specified by:

getSynonyms in interface Term

Returns:

the synonyms

getName

public String getName()

Description copied from interface: Term

Return the name of this term.

Specified by:

getName in interface Term

Returns:

the name of the term

getDescription

public String getDescription()

Description copied from interface: Term

Return a human-readable description of this term, or the empty string if none is available.

Specified by:

getDescription in interface Term

Returns:

the description of the term

setDescription

public void setDescription(String description)

Description copied from interface: Term

set the description of the term;

Specified by:

setDescription in interface Term

getOntology

public Ontology getOntology()

Description copied from interface: OntologyTerm

Get the remote ontology referenced by this term

Specified by:

getOntology in interface OntologyTerm

Specified by:

getOntology in interface Term

Returns:

the ontology

getTargetOntology

public Ontology getTargetOntology()

toString

public String toString()

Overrides:

toString in class Object

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Annotatable

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getChangeSupport

public ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable