org.biojava.ontology
Class Term.Impl

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.ontology.AbstractTerm
          extended by 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.ontology.Term
Term.Impl
 
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from class org.biojava.ontology.AbstractTerm
description
 
Fields inherited from interface org.biojava.ontology.Term
ONTOLOGY
 
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
 
Constructor Summary
Term.Impl(Ontology ontology, String name)
           
Term.Impl(Ontology ontology, String name, String description)
           
Term.Impl(Ontology ontology, String name, String description, Object[] synonyms)
           
 
Method Summary
 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 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.ontology.Term
setDescription
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

Term.Impl

public Term.Impl(Ontology ontology,
                 String name)

Term.Impl

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

Term.Impl

public Term.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 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