Package org.biojavax.ontology

Class SimpleComparableOntology

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.ontology.SimpleComparableOntology

All Implemented Interfaces:

Comparable, Ontology, Changeable, ComparableOntology

public class SimpleComparableOntology
extends AbstractChangeable
implements ComparableOntology

Represents an ontology that can be compared to other ontologies.

Since:

1.5

Author:

Richard Holland, Mark Schreiber

Nested Class Summary

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

Ontology.Impl

Field Summary

Fields inherited from interface org.biojavax.ontology.ComparableOntology

DESCRIPTION, TERM, TRIPLE

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleComparableOntology()
	SimpleComparableOntology(String name)	Creates a new instance of SimpleComparableOntology with the given, immutable, non-nullable name.

Method Summary

Modifier and Type	Method	Description
int	compareTo(Object o)	Ontologies are compared only by name.
boolean	containsTerm(String name)	Determines if this ontology currently contains a term named name
boolean	containsTriple(Term subject, Term object, Term predicate)	See if a triple exists in this ontology
Term	createTerm(String name)	Create a new term in this ontology.
Term	createTerm(String name, String description)	Create a new term in this ontology.
Term	createTerm(String name, String description, Object[] synonyms)	Create a new term in this ontology.
Triple	createTriple(Term subject, Term object, Term predicate, String name, String description)	Creates a new Triple.
Variable	createVariable(String name, String description)	Create a new term in this ontology that is used as a variable.
void	deleteTerm(Term t)	Remove a term from an ontology, together with all triples which refer to it.
boolean	equals(Object obj)	Ontologies are equal if their names are equal.
String	getDescription()	Return a human-readable description of this ontology.
Integer	getId()	Gets the Hibernate ID.
String	getName()	Return the name of this ontology
OntologyOps	getOps()	Return the associated OntologyOps.
ComparableTerm	getOrCreateTerm(String name)	Looks for a term with the given name and returns it.
ComparableTriple	getOrCreateTriple(Term subject, Term object, Term predicate)	Looks for a triple with the given subject object and predicate and returns it.
ComparableTerm	getOrImportTerm(Term term)	Looks for a term with the same name as the given term and returns it.
Term	getTerm(String s)	Fetch the term with the specified name.
Set	getTerms()	Return all the terms in this ontology
Set	getTermSet()	Returns the set of terms in this ontology.
Set	getTriples(Term subject, Term object, Term predicate)	Return all triples from this ontology which match the supplied pattern.
Set	getTripleSet()	Returns the set of triples in this ontology.
int	hashCode()
Term	importTerm(Term t, String localName)	Create a view of a term from another ontology.
void	setDescription(String description)	Sets a human-readable description of this ontology.
void	setId(Integer id)	Sets the Hibernate ID.
void	setName(String name)	Set the name for this ontology
void	setTermSet(Set terms)	Clears out all the terms and populates the ontology with the contents of the set passed.
void	setTripleSet(Set triples)	Clears out all the triples and populates the ontology with the contents of the set passed.
String	toString()	Form: "name"

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

SimpleComparableOntology

public SimpleComparableOntology(String name)

Creates a new instance of SimpleComparableOntology with the given, immutable, non-nullable name.

Parameters:

name - the name of the ontology.

SimpleComparableOntology

protected SimpleComparableOntology()

Method Detail

compareTo

public int compareTo(Object o)

Ontologies are compared only by name.

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object obj)

Ontologies are equal if their names are equal.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Form: "name"

Overrides:

toString in class Object

containsTerm

public boolean containsTerm(String name)

Determines if this ontology currently contains a term named name

Specified by:

containsTerm in interface Ontology

Returns:

true is contained

getTerm

public Term getTerm(String s)
             throws NoSuchElementException

Fetch the term with the specified name.

Specified by:

getTerm in interface Ontology

Parameters:

s - the name of the term

Returns:

The term named name

Throws:

NoSuchElementException - if no term exists with that name

getOrCreateTerm

public ComparableTerm getOrCreateTerm(String name)

Looks for a term with the given name and returns it. If it couldn't be found, then it creates it, adds it to the ontology, then returns it. If the term has to be created, it is added with the description "auto-generated by biojavax".

Specified by:

getOrCreateTerm in interface ComparableOntology

Parameters:

name - the name of the term to look for.

Returns:

the ComparableTerm representing that name.

getOrCreateTriple

public ComparableTriple getOrCreateTriple(Term subject,
                                          Term object,
                                          Term predicate)

Looks for a triple with the given subject object and predicate and returns it. If it couldn't be found, then it creates it, adds it to the ontology, then returns it.

Specified by:

getOrCreateTriple in interface ComparableOntology

Parameters:

subject - the subject of the triple eg apple

object - the object of the triple eg fruit

predicate - the relationship of the triple eg is_a

Returns:

the ComparableTriple representing the object subject and predicate.

getOrImportTerm

public ComparableTerm getOrImportTerm(Term term)

Looks for a term with the same name as the given term and returns it. If it couldn't be found, then it creates it, adds it to the ontology, then returns it.

Specified by:

getOrImportTerm in interface ComparableOntology

Parameters:

term - the term to look for.

Returns:

the ComparableTerm representing that term in this ontology.

createTerm

public Term createTerm(String name,
                       String description,
                       Object[] synonyms)
                throws AlreadyExistsException,
                       ChangeVetoException,
                       IllegalArgumentException

Create a new term in this ontology.

Specified by:

createTerm in interface Ontology

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

synonyms - Some synonyms for this term.

Returns:

The newly created term.

Throws:

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

importTerm

public Term importTerm(Term t,
                       String localName)
                throws ChangeVetoException,
                       IllegalArgumentException

Create a view of a term from another ontology. If the requested term has already been imported under that name, this method returns the existing RemoteTerm object. If the term that is being imported is itself a RemoteTerm instance then first unwrap the term back to the orriginal term it represents and then produce a RemoteTerm from that. If the term being imported orriginated from this ontology, then return that term unaltered. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term. Thus the term becomes a part of this ontology instead of a pointer to another ontology.

Specified by:

importTerm in interface Ontology

Parameters:

t - the Term to import

localName - the local name to import it under, optionally null

Returns:

a Term

Throws:

ChangeVetoException

IllegalArgumentException

See Also:

ComparableTerm

createTriple

public Triple createTriple(Term subject,
                           Term object,
                           Term predicate,
                           String name,
                           String description)
                    throws AlreadyExistsException,
                           ChangeVetoException

Creates a new Triple. If you call this method with plain Terms instead of ComparableTerms, it will import them into the local ontology first. This is done BEFORE the check to see if the triple already exists, as obviously it can't check until it has the right terms to check with. So you may find the terms get imported but the triple does not. Moral of the story: use ComparableTerm objects!

Specified by:

createTriple in interface Ontology

Parameters:

subject - the subject Term

object - the object Term

predicate - the predicate Term

name - the name of the triple, or null

description - the description of the triple, or null

Returns:

a new Triple over these three terms

Throws:

AlreadyExistsException - if a triple already exists with the same subject, object and predicate, regardless of the name and description

ChangeVetoException

See Also:

ComparableTerm

deleteTerm

public void deleteTerm(Term t)
                throws ChangeVetoException

Remove a term from an ontology, together with all triples which refer to it. If you call this method with a plain Term instead of a ComparableTerm, it may not match any of the terms in the ontology as they are all stored as ComparableTerms. So, use ComparableTerm objects! This method also removes all triples that the term is involved in.

Specified by:

deleteTerm in interface Ontology

Throws:

ChangeVetoException

See Also:

ComparableTerm

getTriples

public Set getTriples(Term subject,
                      Term object,
                      Term predicate)

Return all triples from this ontology which match the supplied pattern. If any of the parameters of this method are null, they are treated as wildcards. If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms. So, use ComparableTerm objects! The set returned is a set of ComparableTriple objects.

Specified by:

getTriples in interface Ontology

Parameters:

subject - The subject to search for, or null

object - The object to search for, or null

predicate - The relationship to search for, or null.

Returns:

a Set of triples

See Also:

ComparableTerm, ComparableTriple

setTripleSet

public void setTripleSet(Set triples)
                  throws ChangeVetoException

Clears out all the triples and populates the ontology with the contents 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:

setTripleSet in interface ComparableOntology

Parameters:

triples - the set of ComparableTriple objects this ontology should have.

Throws:

ChangeVetoException - if any of them are unacceptable.

See Also:

ComparableTriple

getTripleSet

public Set getTripleSet()

Returns the set of triples in this ontology. 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:

getTripleSet in interface ComparableOntology

Returns:

the set of ComparableTriple objects.

getTerms

public Set getTerms()

Return all the terms in this ontology This will always return a set of ComparableTerm objects. It is not the original set so you are safe to modify it.

Specified by:

getTerms in interface Ontology

Returns:

a Set of all Terms of the ontology.

See Also:

ComparableTerm

setTermSet

public void setTermSet(Set terms)
                throws ChangeVetoException

Clears out all the terms and populates the ontology with the contents of the set passed. The terms should be ComparableTerms. 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:

setTermSet in interface ComparableOntology

Parameters:

terms - a set of Term objects this ontology should have.

Throws:

ChangeVetoException - if any of them are unacceptable.

See Also:

ComparableTerm

getTermSet

public Set getTermSet()

Returns the set of terms in this ontology. 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:

getTermSet in interface ComparableOntology

Returns:

a set of ComparableTerm objects.

See Also:

ComparableTerm

containsTriple

public boolean containsTriple(Term subject,
                              Term object,
                              Term predicate)

See if a triple exists in this ontology If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms. So, use ComparableTerm objects! The set returned is a set of ComparableTriple objects.

Specified by:

containsTriple in interface Ontology

Returns:

true if contained

See Also:

ComparableTerm, ComparableTriple

createTerm

public Term createTerm(String name)
                throws AlreadyExistsException,
                       ChangeVetoException,
                       IllegalArgumentException

Create a new term in this ontology.

Specified by:

createTerm in interface Ontology

Parameters:

name - The name of the term (must be unique))

Returns:

The newly created term.

Throws:

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

createTerm

public Term createTerm(String name,
                       String description)
                throws AlreadyExistsException,
                       ChangeVetoException,
                       IllegalArgumentException

Create a new term in this ontology.

Specified by:

createTerm in interface Ontology

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

Returns:

The newly created term.

Throws:

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

createVariable

public Variable createVariable(String name,
                               String description)
                        throws AlreadyExistsException,
                               ChangeVetoException,
                               IllegalArgumentException

Create a new term in this ontology that is used as a variable. NOT IMPLEMENTED

Specified by:

createVariable in interface Ontology

Parameters:

name - The name of the term (must be unique)

description - A human-readable description (may be empty)

Returns:

The newly created term.

Throws:

AlreadyExistsException - if a term of this name already exists

ChangeVetoException

IllegalArgumentException - if either name or description is null, or violates some other constraint of this implementation.

getDescription

public String getDescription()

Return a human-readable description of this ontology.

Specified by:

getDescription in interface ComparableOntology

Specified by:

getDescription in interface Ontology

Returns:

the description.

setDescription

public void setDescription(String description)
                    throws ChangeVetoException

Sets a human-readable description of this ontology.

Specified by:

setDescription in interface ComparableOntology

Specified by:

setDescription in interface Ontology

Parameters:

description - the description.

Throws:

ChangeVetoException - in case of problems.

getName

public String getName()

Return the name of this ontology

Specified by:

getName in interface Ontology

Returns:

the name of the ontology

setName

public void setName(String name)

Description copied from interface: Ontology

Set the name for this ontology

Specified by:

setName in interface Ontology

Parameters:

name - - the name

getOps

public OntologyOps getOps()

Return the associated OntologyOps. This method should be implemented by ontology implementors to allow OntoTools to get optimized access to some usefull ontology operations. It is not intended that users will ever invoke this. A sensible dumb implementation of this would return a per-ontology instance of DefaultOps.

Specified by:

getOps in interface Ontology

Returns:

the OntologyOps instance associated with this instance.

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.