org.biojavax.ontology

Class SimpleComparableTriple

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ontology.SimpleComparableTriple

All Implemented Interfaces:

Comparable, Annotatable, Term, Triple, Changeable, ComparableTriple

public class SimpleComparableTriple
extends AbstractChangeable
implements ComparableTriple

Basic comparable triple, BioSQL style.

Since:

1.5

Author:

Richard Holland

Nested Class Summary

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

Triple.Impl

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

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojavax.ontology.ComparableTriple

DESCRIPTOR

Fields inherited from interface org.biojava.ontology.Term

ONTOLOGY

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleComparableTriple()

Method Summary

Methods

Modifier and Type	Method and Description
void	addDescriptor(ComparableTerm desc) Adds a descriptor.
void	addSynonym(Object synonym) Add a synonym for this term.
int	compareTo(Object o) Triples are sorted in order of ontology, subject, object, and finally predicate.
boolean	equals(Object o) Check to see if an object is an equivalent Triple.
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.
Set	getDescriptors() Returns all descriptors.
Integer	getId() Gets the Hibernate ID.
String	getName() Return the name of this term.
Term	getObject() Return the object term of this triple.
Ontology	getOntology() Return the ontology in which this term exists.
Term	getPredicate() Return a Term which defines the type of relationship between the subject and object terms.
Term	getSubject() Return the subject term of this triple
Object[]	getSynonyms() Return the synonyms for this term.
int	hashCode() The hashcode for a Triple.
boolean	removeDescriptor(ComparableTerm desc) Removes a descriptor.
void	removeSynonym(Object synonym) Remove a synonym for this term.
void	setDescription(String desc) set the description of the term;
void	setDescriptors(Set descriptors) Clears the current set of descriptors and replaces it with the content of the set passed.
void	setId(Integer id) Sets the Hibernate ID.
String	toString() Form: "ontology:predicate(subject,object)"

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

SimpleComparableTriple

protected SimpleComparableTriple()

Method Detail

compareTo

public int compareTo(Object o)

Triples are sorted in order of ontology, subject, object, and finally predicate.

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object o)

Check to see if an object is an equivalent Triple.

Two triples are equivalent if they have the same subject, object and predicate fields.

 if (! (o instanceof Triple)) {
     return false;
 }
 Triple to = (Triple) o;
 return to.getSubject() == getSubject() &&
        to.getObject() == getObject() &&
        to.getPredicate() == getPredicate();
 

If you do not implement equals in this way then you have no guarantee that your Triple objects will be found in an ontology and that they will not be duplicated.

Triples are equal only if they are from the same ontology and share the same subject, object and predicate.

Specified by:

equals in interface Triple

Overrides:

equals in class Object

hashCode

public int hashCode()

The hashcode for a Triple.

This must be implemented as:

 return getSubject().hashCode() +
   31 * getObject().hashCode() +
   31 * 31 * getPredicate().hashCode();
 

If you do not implement hashcode in this way then you have no guarantee that your Triple objects will be found in an ontology and that they will not be duplicated.

Specified by:

hashCode in interface Triple

Overrides:

hashCode in class Object

getName

public String getName()

Return the name of this term. Returns the output of toSring()

Specified by:

getName in interface Term

Returns:

the name of the term

getSubject

public Term getSubject()

Return the subject term of this triple

Specified by:

getSubject in interface Triple

Returns:

the subject term

getObject

public Term getObject()

Return the object term of this triple.

Specified by:

getObject in interface Triple

Returns:

the object term

getPredicate

public Term getPredicate()

Return a Term which defines the type of relationship between the subject and object terms.

Specified by:

getPredicate in interface Triple

Returns:

the predicate

addDescriptor

public void addDescriptor(ComparableTerm desc)
                   throws IllegalArgumentException,
                          ChangeVetoException

Adds a descriptor. Must not be null.

Specified by:

addDescriptor in interface ComparableTriple

Parameters:

desc - the descriptor to add.

Throws:

IllegalArgumentException - if the descriptor is missing.

ChangeVetoException - in case of objections.

removeDescriptor

public boolean removeDescriptor(ComparableTerm desc)
                         throws IllegalArgumentException,
                                ChangeVetoException

Removes a descriptor. Must not be null.

Specified by:

removeDescriptor in interface ComparableTriple

Parameters:

desc - the descriptor to remove.

Returns:

True if it did it, false if the descriptor did not exist.

Throws:

IllegalArgumentException - if the descriptor is missing.

ChangeVetoException - in case of objections.

getDescriptors

public Set getDescriptors()

Returns all descriptors. 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:

getDescriptors in interface ComparableTriple

Returns:

a set of all ComparableTerm descriptors, possibly empty.

See Also:

ComparableTerm

setDescriptors

public void setDescriptors(Set descriptors)
                    throws ChangeVetoException

Clears the current set of descriptors and replaces it with the content of the set passed. 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:

setDescriptors in interface ComparableTriple

Parameters:

descriptors - the set of ComparableTerm descriptors to add.

Throws:

ChangeVetoException - in case of objections.

See Also:

ComparableTerm

removeSynonym

public void removeSynonym(Object synonym)

Remove a synonym for this term. NOT IMPLEMENTED

Specified by:

removeSynonym in interface Term

addSynonym

public void addSynonym(Object synonym)

Add a synonym for this term. NOT IMPLEMENTED

Specified by:

addSynonym in interface Term

Parameters:

synonym - the synonym

getSynonyms

public Object[] getSynonyms()

Return the synonyms for this term. ALWAYS RETURNS AN EMPTY LIST

Specified by:

getSynonyms in interface Term

Returns:

the synonyms

getOntology

public Ontology getOntology()

Return the ontology in which this term exists.

Specified by:

getOntology in interface Term

Returns:

the ontology

getDescription

public String getDescription()

Return a human-readable description of this term, or the empty string if none is available. ALWAYS RETURNS THE EMPTY STRING

Specified by:

getDescription in interface Term

Returns:

the description of the term

setDescription

public void setDescription(String desc)

set the description of the term; does not do anything

Specified by:

setDescription in interface Term

getAnnotation

public Annotation getAnnotation()

Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

toString

public String toString()

Form: "ontology:predicate(subject,object)"

Overrides:

toString in class Object

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.