Package org.biojava.ontology

Class Term.Impl

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.ontology.AbstractTerm

org.biojava.ontology.Term.Impl

All Implemented Interfaces:

Serializable, Annotatable, Term, Changeable

Direct Known Subclasses:

Variable.Impl

Enclosing interface:

Term

public static class Term.Impl
extends AbstractTerm
implements Term, Serializable

Simple in-memory implementation of an ontology term.

See Also:

This can be used to implement Ontology.createTerm, Serialized Form

Nested Class Summary

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

Annotatable.AnnotationForwarder

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

Term.Impl

Field Summary

Fields inherited from class org.biojava.ontology.AbstractTerm

description

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.ontology.Term

ONTOLOGY

Constructor Summary

Constructors

Constructor	Description
Impl(Ontology ontology, String name)
Impl(Ontology ontology, String name, String description)
Impl(Ontology ontology, String name, String description, Object[] synonyms)

Method Summary

Modifier and Type	Method	Description
void	addSynonym(Object synonym)	Add a synonym for this term.
boolean	equals(Object obj)
Annotation	getAnnotation()	Should return the associated annotation 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()	Return the ontology in which this term exists.
Object[]	getSynonyms()	Return the synonyms for this term.
int	hashCode()
void	removeSynonym(Object synonym)	Remove a synonym for this term.
void	setAnnotation(Annotation annotation)
void	setSynonyms(Set<Object> synonyms)
String	toString()

Methods inherited from class org.biojava.ontology.AbstractTerm

getChangeSupport, setDescription

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.ontology.Term

setDescription

Constructor Detail

Impl

public Impl(Ontology ontology,
            String name)

Impl

public Impl(Ontology ontology,
            String name,
            String description)

Impl

public Impl(Ontology ontology,
            String name,
            String description,
            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

setAnnotation

public void setAnnotation(Annotation annotation)

setSynonyms

public void setSynonyms(Set<Object> synonyms)

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

getOntology

public Ontology getOntology()

Description copied from interface: Term

Return the ontology in which this term exists.

Specified by:

getOntology in interface Term

Returns:

the ontology

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

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object