Uses of Interface
org.biojava.ontology.Ontology

Packages that use Ontology
org.biojava.bio.program.gff3 Support for reading and writing GFF3. 
org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. 
org.biojava.ontology A general-purpose API for ontologies. 
org.biojava.ontology.io Tools for loading and saving ontologies. 
org.biojava.ontology.obo   
org.biojavax.ontology Extensions to the biojava ontology model that represent BioSQL ontology. 
 

Uses of Ontology in org.biojava.bio.program.gff3
 

Methods in org.biojava.bio.program.gff3 with parameters of type Ontology
protected  GFF3Record GFF3Parser.createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack)
          Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
 void GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology)
          Informs handler of each line of gff read from bReader.
 void GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator)
          Informs handler of each line of GFF read from bReader
protected  void GFF3Parser.parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack)
          Parse attValList into a Map of attributes and value lists.
 

Uses of Ontology in org.biojava.bio.seq.db.biosql
 

Methods in org.biojava.bio.seq.db.biosql that return Ontology
 Ontology BioSQLSequenceDB.addOntology(Ontology onto)
          Deprecated.  
 Ontology BioSQLSequenceDB.createOntology(String name, String description)
          Deprecated.  
 Ontology BioSQLSequenceDB.getOntology(String name)
          Deprecated.  
 

Methods in org.biojava.bio.seq.db.biosql with parameters of type Ontology
 Ontology BioSQLSequenceDB.addOntology(Ontology onto)
          Deprecated.  
 

Uses of Ontology in org.biojava.ontology
 

Classes in org.biojava.ontology that implement Ontology
 class IntegerOntology
           
static class Ontology.Impl
          A basic in-memory implementation of an ontology
 

Methods in org.biojava.ontology that return Ontology
 Ontology OntologyFactory.createOntology(String name, String description)
          Creates a new Ontology
static Ontology OntoTools.getCoreOntology()
          Get the Ontology that defines our core "central dogma".
 Ontology Triple.Impl.getOntology()
           
 Ontology Term.getOntology()
          Return the ontology in which this term exists.
 Ontology Term.Impl.getOntology()
           
 Ontology RemoteTerm.Impl.getOntology()
           
 Ontology OntologyTerm.getOntology()
          Get the remote ontology referenced by this term
 Ontology OntologyTerm.Impl.getOntology()
           
 Ontology IntegerOntology.IntTerm.getOntology()
           
 Ontology OntologyTerm.Impl.getTargetOntology()
           
 

Methods in org.biojava.ontology with parameters of type Ontology
 OntologyTerm Ontology.Impl.createOntologyTerm(Ontology o)
           
 

Constructors in org.biojava.ontology with parameters of type Ontology
OntologyTerm.Impl(Ontology ontology, Ontology target)
           
OntologyTerm.Impl(Ontology ontology, Ontology target, Object[] synonyms)
           
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name)
           
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
           
Term.Impl(Ontology ontology, String name)
           
Term.Impl(Ontology ontology, String name, String description)
           
Term.Impl(Ontology ontology, String name, String description, Object[] synonyms)
           
Variable.Impl(Ontology ontology, String name, String description)
           
Variable.Impl(Ontology ontology, String name, String description, Object[] synonyms)
           
 

Uses of Ontology in org.biojava.ontology.io
 

Methods in org.biojava.ontology.io that return Ontology
 Ontology TabDelimParser.parse(BufferedReader in, OntologyFactory of)
          Parse an ontology from a reader.
 Ontology GOParser.parseGO(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory)
           
 Ontology OboParser.parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription)
          Parse a OBO file and return its content as a BioJava Ontology object
 

Uses of Ontology in org.biojava.ontology.obo
 

Constructors in org.biojava.ontology.obo with parameters of type Ontology
OboFileHandler(Ontology ontology)
           
 

Uses of Ontology in org.biojavax.ontology
 

Subinterfaces of Ontology in org.biojavax.ontology
 interface ComparableOntology
          An Ontology that can be compared to another.
 

Classes in org.biojavax.ontology that implement Ontology
 class SimpleComparableOntology
          Represents an ontology that can be compared to other ontologies.
 

Methods in org.biojavax.ontology that return Ontology
 Ontology SimpleComparableTriple.getOntology()
          Return the ontology in which this term exists.
 Ontology SimpleComparableTerm.getOntology()
          Return the ontology in which this term exists.