Package org.biojava.nbio.ontology

Class Ontology.Impl

java.lang.Object

org.biojava.nbio.ontology.Ontology.Impl

All Implemented Interfaces:

Serializable, Ontology

Enclosing interface:

Ontology

public static final class Ontology.Impl
extends Object
implements Ontology, Serializable

A basic in-memory implementation of an ontology

Since:

1.3

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

Ontology.Impl

Constructor Summary

Constructors

Constructor	Description
Impl(String name, String description)

Method Summary

Modifier and Type	Method	Description
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
OntologyTerm	createOntologyTerm(Ontology o)
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.
String	getDescription()	Return a human-readable description of this ontology, or the empty string if none is available
String	getName()	Return the name of this ontology
OntologyOps	getOps()	Return the associated OntologyOps.
Term	getTerm(String name)	Fetch the term with the specified name.
Set<Term>	getTerms()	Return all the terms in this ontology
Set<Triple>	getTriples(Term subject, Term object, Term predicate)	Return all triples from this ontology which match the supplied pattern.
Term	importTerm(Term t, String name)	Create a view of a term from another ontology.
void	setDescription(String description)	set the description of this ontology
void	setName(String name)	Set the name for this ontology
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Impl

public Impl(String name,
            String description)

Method Detail

getName

public String getName()

Description copied from interface: Ontology

Return the name of this ontology

Specified by:

getName in interface Ontology

Returns:

the name of the ontology

getDescription

public String getDescription()

Description copied from interface: Ontology

Return a human-readable description of this ontology, or the empty string if none is available

Specified by:

getDescription in interface Ontology

Returns:

the description of the term

setDescription

public void setDescription(String description)

Description copied from interface: Ontology

set the description of this ontology

Specified by:

setDescription in interface Ontology

getTerms

public Set<Term> getTerms()

Description copied from interface: Ontology

Return all the terms in this ontology

Specified by:

getTerms in interface Ontology

Returns:

a Set of all Terms of the ontology.

getTerm

public Term getTerm(String name)
             throws NoSuchElementException

Description copied from interface: Ontology

Fetch the term with the specified name.

Specified by:

getTerm in interface Ontology

Parameters:

name - the name of the term

Returns:

The term named name

Throws:

NoSuchElementException - if no term exists with that name

getTriples

public Set<Triple> getTriples(Term subject,
                              Term object,
                              Term predicate)

Description copied from interface: Ontology

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.

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

createTerm

public Term createTerm(String name)
                throws AlreadyExistsException,
                       IllegalArgumentException

Description copied from interface: Ontology

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

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,
                       IllegalArgumentException

Description copied from interface: Ontology

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

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

createTerm

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

Description copied from interface: Ontology

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

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,
                               IllegalArgumentException

Description copied from interface: Ontology

Create a new term in this ontology that is used as a variable.

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

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

createOntologyTerm

public OntologyTerm createOntologyTerm(Ontology o)
                                throws AlreadyExistsException

Throws:

AlreadyExistsException

importTerm

public Term importTerm(Term t,
                       String name)
                throws IllegalArgumentException

Description copied from interface: Ontology

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.

Specified by:

importTerm in interface Ontology

Parameters:

t - the Term to import

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

Returns:

a Term

Throws:

IllegalArgumentException

deleteTerm

public void deleteTerm(Term t)

Description copied from interface: Ontology

Remove a term from an ontology, together with all triples which refer to it.

Specified by:

deleteTerm in interface Ontology

containsTerm

public boolean containsTerm(String name)

Description copied from interface: Ontology

Determines if this ontology currently contains a term named name

Specified by:

containsTerm in interface Ontology

Returns:

true is contained

containsTriple

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

Description copied from interface: Ontology

See if a triple exists in this ontology

Specified by:

containsTriple in interface Ontology

Returns:

true if contained

createTriple

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

Description copied from interface: Ontology

Creates a new Triple.

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

IllegalArgumentException - if subject, object or predicate are not all from the same ontology

NullPointerException - if subject, object or predicate are null

getOps

public OntologyOps getOps()

Description copied from interface: Ontology

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.

toString

public String toString()

Overrides:

toString in class Object

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