Package org.biojavax.ontology

Class SimpleComparableTerm

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ontology.SimpleComparableTerm

All Implemented Interfaces:

Comparable, Annotatable, Term, Changeable, ComparableTerm, RankedCrossRefable

public class SimpleComparableTerm
extends AbstractChangeable
implements ComparableTerm

A Term object that can be compared and thus sorted.

Since:

1.5

Author:

Richard Holland

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 interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojavax.ontology.ComparableTerm

DESCRIPTION, IDENTIFIER, OBSOLETE, RANKEDCROSSREF

Fields inherited from interface org.biojava.ontology.Term

ONTOLOGY

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleComparableTerm()

Method Summary

Modifier and Type	Method	Description
void	addRankedCrossRef(RankedCrossRef crossref)	Adds a ranked cross reference to the existing set.
void	addSynonym(Object synonym)	Add a synonym for this term.
int	compareTo(Object o)	Terms are sorted by ontology first, then name.
boolean	equals(Object obj)	Two terms are equal if they are in the same ontology and share the same name.
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.
Integer	getId()	Gets the Hibernate ID.
String	getIdentifier()	Returns the (optional) identifier associated with this term.
String	getName()	Return the name of this term.
Boolean	getObsolete()	Checks to see if this term is obsolete.
Ontology	getOntology()	Return the ontology in which this term exists.
Set	getRankedCrossRefs()	Returns the set of all ranked cross references associated with an object.
Object[]	getSynonyms()	Return the synonyms for this term.
int	hashCode()
void	removeRankedCrossRef(RankedCrossRef crossref)	Removes a ranked cross reference from the existing set.
void	removeSynonym(Object synonym)	Remove a synonym for this term.
void	setDescription(String description)	Sets the description associated with this term.
void	setId(Integer id)	Sets the Hibernate ID.
void	setIdentifier(String identifier)	Sets the (optional) identifier associated with this term.
void	setObsolete(Boolean obsolete)	Sets the obsolescence flag associated with this term.
void	setRankedCrossRefs(Set rankedcrossrefs)	Sets the ranked cross references associated with an object.
String	toString()	Form: "ontology:name [obsolete]" where [obsolete] is optional

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, 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

Constructor Detail

SimpleComparableTerm

protected SimpleComparableTerm()

Method Detail

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.