Class SimpleComparableTerm

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.ontology.SimpleComparableTerm
All Implemented Interfaces:
Comparable, Annotatable, Term, Changeable, ComparableTerm, RankedCrossRefable

A Term object that can be compared and thus sorted.
Since:
1.5
Author:
Richard Holland
  • Constructor Details

  • 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
      Parameters:
      synonym -
    • getSynonyms

      public Object[] getSynonyms()
      Return the synonyms for this term.
      Specified by:
      getSynonyms in interface Term
      Returns:
      the synonyms
    • 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

      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

      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

      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

      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

      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.