Uses of Class
phenote.datamodel.Ontology

Packages that use Ontology

phenote.config
phenote.datamodel
phenote.gui
phenote.gui.field
phenote.servlet

Uses of Ontology in phenote.config

Methods in phenote.config that return types with arguments of type Ontology

java.util.List<Ontology>

Config.getAllOntologies()

Methods in phenote.config with parameters of type Ontology

void	Config.addOntology(Ontology o)

Method parameters in phenote.config with type arguments of type Ontology

void	Config.setAllOntologies(java.util.List<Ontology> onts)

Uses of Ontology in phenote.datamodel

Methods in phenote.datamodel that return Ontology

Ontology	CharFieldManager.getComparisonRelationOntology() Return ontology to use for statement comparisons this needs work.
Ontology	CharField.getFirstOntology()
Ontology	CharField.getOntology()
Ontology	CharFieldManager.getOntologyForName(java.lang.String ontologyName) Returns ontology with name, null if not found
Ontology	CharField.getOntologyForName(java.lang.String ontologyName) Returns Ontology with name ontologyName (ignores case), ont ex if dont have it
Ontology	CharFieldManager.getOntologyForTerm(org.obo.datamodel.OBOClass term) Currently iterates through every ontology looking for term, if this proves too inefficient we could do something with ID prefixes
Ontology	CharField.getPostCompRelOntol()

Methods in phenote.datamodel that return types with arguments of type Ontology

java.util.List<Ontology>	CharFieldManager.getAllOntologies()
java.util.List<Ontology>	CharField.getOntologyList()

Methods in phenote.datamodel with parameters of type Ontology

void	CharField.addOntology(Ontology o)
void	CharField.setPostCompRelOntol(Ontology o)

Uses of Ontology in phenote.gui

Fields in phenote.gui with type parameters of type Ontology

(package private) java.util.List<Ontology>

GetInfo.loadedOntologies

Uses of Ontology in phenote.gui.field

Methods in phenote.gui.field with parameters of type Ontology

void	CompListSearcher.setOntology(Ontology o) Set the ontology to search.

Method parameters in phenote.gui.field with type arguments of type Ontology

void	CompListSearcher.setOntologies(java.util.List<Ontology> l)

Constructors in phenote.gui.field with parameters of type Ontology

CompListSearcher(Ontology o)
Ontology - the initial ontology to search, setOntology changes this, initially only searches the one ontology (not ALL) - used by servlet which currently doesnt do ALL

Constructor parameters in phenote.gui.field with type arguments of type Ontology

CompListSearcher(java.util.List<Ontology> l)
l - initial list of ontologies to search, as in ALL.

Uses of Ontology in phenote.servlet

Methods in phenote.servlet that return types with arguments of type Ontology

java.util.List<Ontology>

AdminBean.getOntologies()

Method parameters in phenote.servlet with type arguments of type Ontology

void	AdminBean.setOntologies(java.util.List<Ontology> ontologies)