Class SimpleComparableTerm

Method Details

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object

• equals

  public boolean equals(Object obj)

  Two terms are equal if they are in the same ontology and share the same name.

  Overrides:

  equals in class Object

• compareTo

  public int compareTo(Object o)

  Terms are sorted by ontology first, then name.

  Specified by:

  compareTo in interface Comparable

• addSynonym

  public void addSynonym(Object synonym)

  Add a synonym for this term. Synonyms are stored in the database as the results of a toString() operation on each synonym object. This doesn't happen until it reaches the database though, so if you are not using a database, don't worry about it.

  Specified by:

  addSynonym in interface Term

  Parameters:

  synonym - the synonym

• removeSynonym

  public void removeSynonym(Object synonym)

  Remove a synonym for this term.

  Specified by:

  removeSynonym in interface Term

• getSynonyms

  public Object[] getSynonyms()

  Return the synonyms for this term.

  Specified by:

  getSynonyms in interface Term

  Returns:

  the synonyms

• getRankedCrossRefs

  public Set getRankedCrossRefs()

  Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:

  getRankedCrossRefs in interface RankedCrossRefable

  Returns:

  a set of RankedCrossRef objects.

• setRankedCrossRefs

  public void setRankedCrossRefs(Set rankedcrossrefs) throws ChangeVetoException

  Sets the ranked cross references associated with an object. Null will throw an exception but the empty set is fine. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:

  setRankedCrossRefs in interface RankedCrossRefable

  Parameters:

  rankedcrossrefs - a set of RankedCrossRef objects.

  Throws:

  ChangeVetoException - if the set was null or any of its contents were not RankedCrossRef objects.

• addRankedCrossRef

  public void addRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException

  Adds a ranked cross reference to the existing set. If already present, this call is ignored. Null values are not acceptable.

  Specified by:

  addRankedCrossRef in interface RankedCrossRefable

  Parameters:

  crossref - the ranked cross reference to add.

  Throws:

  ChangeVetoException - if the parameter is null.

• removeRankedCrossRef

  public void removeRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException

  Removes a ranked cross reference from the existing set. If not present, this call is ignored. Null values are not acceptable.

  Specified by:

  removeRankedCrossRef in interface RankedCrossRefable

  Parameters:

  crossref - the ranked cross reference to remove.

  Throws:

  ChangeVetoException - if the parameter is null.

• getName

  public String getName()

  Return the name of this term.

  Specified by:

  getName in interface Term

  Returns:

  the name of the term

• getDescription

  public String getDescription()

  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) throws ChangeVetoException

  Sets the description associated with this term.

  Specified by:

  setDescription in interface ComparableTerm

  Specified by:

  setDescription in interface Term

  Parameters:

  description - the description to give the term. Nullable.

  Throws:

  ChangeVetoException - if the description is unacceptable.

• getOntology

  public Ontology getOntology()

  Return the ontology in which this term exists.

  Specified by:

  getOntology in interface Term

  Returns:

  the ontology

• toString

  public String toString()

  Form: "ontology:name [obsolete]" where [obsolete] is optional

  Overrides:

  toString in class Object

• getAnnotation

  public Annotation getAnnotation()

  Should return the associated annotation object. ALWAYS RETURNS AN EMPTY ANNOTATION OBJECT

  Specified by:

  getAnnotation in interface Annotatable

  Returns:

  an Annotation object, never null

• getIdentifier

  public String getIdentifier()

  Returns the (optional) identifier associated with this term.

  Specified by:

  getIdentifier in interface ComparableTerm

  Returns:

  the string identifier.

• setIdentifier

  public void setIdentifier(String identifier) throws ChangeVetoException

  Sets the (optional) identifier associated with this term.

  Specified by:

  setIdentifier in interface ComparableTerm

  Parameters:

  identifier - the identifier to give the term. Null will unset it.

  Throws:

  ChangeVetoException - if the identifier is unacceptable.

• getObsolete

  public Boolean getObsolete()

  Checks to see if this term is obsolete. As the column in the database is nullable, this value is a Boolean object instead of a boolean simple type. Hence it may also be null.

  Specified by:

  getObsolete in interface ComparableTerm

  Returns:

  true if it is, false if not.

• setObsolete

  public void setObsolete(Boolean obsolete) throws ChangeVetoException

  Sets the obsolescence flag associated with this term.

  Specified by:

  setObsolete in interface ComparableTerm

  Parameters:

  obsolete - true if it is obsolete, false if not. Nullable.

  Throws:

  ChangeVetoException - if the change is unacceptable.

• getId

  public Integer getId()

  Gets the Hibernate ID. Should be used with caution.

  Returns:

  the Hibernate ID, if using Hibernate.

• setId

  public void setId(Integer id)

  Sets the Hibernate ID. Should be used with caution.

  Parameters:

  id - the Hibernate ID, if using Hibernate.