Package org.biojavax.ontology

Interface ComparableOntology

All Superinterfaces:

Changeable, Comparable, Ontology

All Known Implementing Classes:

SimpleComparableOntology

public interface ComparableOntology
extends Ontology, Comparable, Changeable

An Ontology that can be compared to another.

Since:

1.5

Author:

Richard Holland

See Also:

ComparableTerm, ComparableTriple

Nested Class Summary

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

Ontology.Impl

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	DESCRIPTION
static ChangeType	TERM
static ChangeType	TRIPLE

Method Summary

Modifier and Type	Method	Description
String	getDescription()	Return a human-readable description of this ontology.
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.
Set	getTermSet()	Returns the set of terms in this ontology.
Set	getTripleSet()	Returns the set of triples in this ontology.
void	setDescription(String description)	Sets a human-readable description of 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.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojava.ontology.Ontology

containsTerm, containsTriple, createTerm, createTerm, createTerm, createTriple, createVariable, deleteTerm, getName, getOps, getTerm, getTerms, getTriples, importTerm, setName

Field Detail

TERM

static final ChangeType TERM

TRIPLE

static final ChangeType TRIPLE

DESCRIPTION

static final ChangeType DESCRIPTION

Method Detail

setDescription

void setDescription(String description)
             throws ChangeVetoException

Sets a human-readable description of this ontology.

Specified by:

setDescription in interface Ontology

Parameters:

description - the description.

Throws:

ChangeVetoException - in case of problems.

getDescription

String getDescription()

Return a human-readable description of this ontology.

Specified by:

getDescription in interface Ontology

Returns:

the description.

setTermSet

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.

Parameters:

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

Throws:

ChangeVetoException - if any of them are unacceptable.

See Also:

ComparableTerm

getTermSet

Set getTermSet()

Returns the set of terms in this ontology.

Returns:

a set of ComparableTerm objects.

See Also:

ComparableTerm

setTripleSet

void setTripleSet(Set triples)
           throws ChangeVetoException

Clears out all the triples and populates the ontology with the contents of the set passed.

Parameters:

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

Throws:

ChangeVetoException - if any of them are unacceptable.

See Also:

ComparableTriple

getTripleSet

Set getTripleSet()

Returns the set of triples in this ontology.

Returns:

the set of ComparableTriple objects.

getOrCreateTerm

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.

Parameters:

name - the name of the term to look for.

Returns:

the ComparableTerm representing that name.

getOrCreateTriple

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.

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

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.

Parameters:

term - the term to look for.

Returns:

the ComparableTerm representing that term in this ontology.