All Implemented Interfaces:

Serializable, Ontology, Changeable

Enclosing interface:

Ontology

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

Since:

1.3

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

• Nested Class Summary

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

    Ontology.Impl

• Field Summary

  • Fields inherited from interface org.biojava.ontology.Ontology

    TERM, TRIPLE

• Constructor Summary

  Constructors

  Constructor and Description
  Impl (String name, String description)

• Method Summary

  All Methods

  Modifier and Type	Method and 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 org.biojava.utils.AbstractChangeable

    addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

  • Methods inherited from class java.lang.Object

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

  • Methods inherited from interface org.biojava.utils.Changeable

    addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

• 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,
     ChangeVetoException 

    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.

    ChangeVetoException

  • createTerm

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

    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.

    ChangeVetoException

  • createTerm

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

    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.

    ChangeVetoException

  • createVariable

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

    ChangeVetoException

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

  • createOntologyTerm

    public OntologyTerm createOntologyTerm(Ontology o)
     throws AlreadyExistsException,
     ChangeVetoException 

    Throws:

    AlreadyExistsException

    ChangeVetoException

  • importTerm

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

    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

    ChangeVetoException

  • deleteTerm

    public void deleteTerm(Term t)
     throws ChangeVetoException 

    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

    Throws:

    ChangeVetoException

  • 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,
     ChangeVetoException,
     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

    ChangeVetoException

    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