Interface Ontology

  • All Known Implementing Classes:
    IntegerOntology, Ontology.Impl

    public interface Ontology
    An ontology.

    This is just a set of Term objects, and a set of Triple objects describing relationships between these terms. This class does not itself contain any reasoning functionality. Ontology is a collection of facts, or axioms.

    Since:
    1.4
    Author:
    Thomas Down, Matthew Pocock
    See Also:
    org.biojavax.ontology.ComparableOntology
    • Method Detail

      • getName

        String getName()
        Return the name of this ontology
        Returns:
        the name of the ontology
      • setName

        void setName​(String name)
        Set the name for this ontology
        Parameters:
        name - - the name
      • getDescription

        String getDescription()
        Return a human-readable description of this ontology, or the empty string if none is available
        Returns:
        the description of the term
      • setDescription

        void setDescription​(String description)
        set the description of this ontology
        Parameters:
        description -
      • getTerms

        Set<TermgetTerms()
        Return all the terms in this ontology
        Returns:
        a Set of all Terms of the ontology.
      • getTriples

        Set<TriplegetTriples​(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.
        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
      • getOps

        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.
        Returns:
        the OntologyOps instance associated with this instance.
      • importTerm

        Term importTerm​(Term t,
                        String localName)
                 throws 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.
        Parameters:
        t - the Term to import
        localName - the local name to import it under, optionally null
        Returns:
        a Term
        Throws:
        ChangeVetoException
        IllegalArgumentException
      • createTriple

        Triple createTriple​(Term subject,
                            Term object,
                            Term predicate,
                            String name,
                            String description)
                     throws AlreadyExistsException
        Creates a new Triple.
        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
        NullPointerException - if subject, object or predicate are null
        IllegalArgumentException - if subject, object or predicate are not all from the same ontology
      • containsTriple

        boolean containsTriple​(Term subject,
                               Term object,
                               Term predicate)
        See if a triple exists in this ontology
        Parameters:
        subject -
        object -
        predicate -
        Returns:
        true if contained
      • deleteTerm

        void deleteTerm​(Term t)
        Remove a term from an ontology, together with all triples which refer to it.
        Parameters:
        t -
        Throws:
        ChangeVetoException
      • containsTerm

        boolean containsTerm​(String name)
        Determines if this ontology currently contains a term named name
        Parameters:
        name -
        Returns:
        true is contained