Uses of Interface
org.biojava.ontology.Ontology
Packages that use Ontology
Package
Description
Support for reading and writing GFF3.
General purpose Sequence storage in a relational database.
A general-purpose API for ontologies.
Tools for loading and saving ontologies.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Uses of Ontology in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 with parameters of type OntologyModifier and TypeMethodDescriptionprotected 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 bReaderprotected 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 OntologyModifier and TypeMethodDescriptionBioSQLSequenceDB.addOntology
(Ontology onto) Deprecated.BioSQLSequenceDB.createOntology
(String name, String description) Deprecated.BioSQLSequenceDB.getOntology
(String name) Deprecated.Methods in org.biojava.bio.seq.db.biosql with parameters of type Ontology -
Uses of Ontology in org.biojava.ontology
Classes in org.biojava.ontology that implement OntologyModifier and TypeClassDescriptionclass
static final class
A basic in-memory implementation of an ontologyMethods in org.biojava.ontology that return OntologyModifier and TypeMethodDescriptionOntologyFactory.createOntology
(String name, String description) Creates a new Ontologystatic Ontology
OntoTools.getCoreOntology()
Get the Ontology that defines our core "central dogma".IntegerOntology.IntTerm.getOntology()
OntologyTerm.getOntology()
Get the remote ontology referenced by this termOntologyTerm.Impl.getOntology()
RemoteTerm.Impl.getOntology()
Term.getOntology()
Return the ontology in which this term exists.Term.Impl.getOntology()
Triple.Impl.getOntology()
OntologyTerm.Impl.getTargetOntology()
Methods in org.biojava.ontology with parameters of type OntologyConstructors in org.biojava.ontology with parameters of type OntologyModifierConstructorDescription -
Uses of Ontology in org.biojava.ontology.io
Methods in org.biojava.ontology.io that return OntologyModifier and TypeMethodDescriptionTabDelimParser.parse
(BufferedReader in, OntologyFactory of) Parse an ontology from a reader.GOParser.parseGO
(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory) 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 -
Uses of Ontology in org.biojavax.ontology
Subinterfaces of Ontology in org.biojavax.ontologyModifier and TypeInterfaceDescriptioninterface
An Ontology that can be compared to another.Classes in org.biojavax.ontology that implement OntologyModifier and TypeClassDescriptionclass
Represents an ontology that can be compared to other ontologies.Methods in org.biojavax.ontology that return OntologyModifier and TypeMethodDescriptionSimpleComparableTerm.getOntology()
Return the ontology in which this term exists.SimpleComparableTriple.getOntology()
Return the ontology in which this term exists.