Uses of Class
org.molgenis.omx.observ.target.OntologyTerm

Packages that use OntologyTerm

Package	Description
org.molgenis.omx.auth
org.molgenis.omx.observ
org.molgenis.omx.observ.target
org.molgenis.omx.observ.target.db
org.molgenis.service

Uses of OntologyTerm in org.molgenis.omx.auth

Subclasses of OntologyTerm in org.molgenis.omx.auth

Modifier and Type	Class and Description
class	PersonRole PersonRole: Seperate type of ontologyTerm to administrate roles.

Uses of OntologyTerm in org.molgenis.omx.observ

Methods in org.molgenis.omx.observ that return OntologyTerm

Modifier and Type	Method and Description
OntologyTerm	Category.getDefinition() Get the The category that is being measured in a specific way..
OntologyTerm	Category.getDefinition(Database db) Deprecated.
OntologyTerm	ObservableFeature_Definitions.getDefinitions() Get the .
OntologyTerm	ObservableFeature_Definitions.getDefinitions(Database db) Deprecated.
OntologyTerm	Protocol.getProtocolType() Get the classification of protocol.
OntologyTerm	Protocol.getProtocolType(Database db) Deprecated.
OntologyTerm	ObservableFeature.getUnit() Get the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).
OntologyTerm	ObservableFeature.getUnit(Database db) Deprecated.

Methods in org.molgenis.omx.observ that return types with arguments of type OntologyTerm

Modifier and Type	Method and Description
List<OntologyTerm>	ObservableFeature.getDefinitions() Get the The concept that is being measured in a specific way..
List<OntologyTerm>	ObservableFeature.getDefinitions(Database db) Deprecated.

Methods in org.molgenis.omx.observ with parameters of type OntologyTerm

Modifier and Type	Method and Description
void	Category.setDefinition(OntologyTerm definition) Set the The category that is being measured in a specific way..
void	ObservableFeature.setDefinitions(OntologyTerm... definitions)
void	ObservableFeature_Definitions.setDefinitions(OntologyTerm definitions) Set the .
void	Protocol.setProtocolType(OntologyTerm protocolType) Set the classification of protocol.
void	ObservableFeature.setUnit(OntologyTerm unit) Set the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).

Method parameters in org.molgenis.omx.observ with type arguments of type OntologyTerm

Modifier and Type	Method and Description
void	ObservableFeature.setDefinitions(List<OntologyTerm> definitions) Set the The concept that is being measured in a specific way..

Uses of OntologyTerm in org.molgenis.omx.observ.target

Subclasses of OntologyTerm in org.molgenis.omx.observ.target

Modifier and Type	Class and Description
class	Accession Accession: An external identifier for an annotation.
class	Species Species: Ontology terms for species.

Methods in org.molgenis.omx.observ.target that return OntologyTerm

Modifier and Type	Method and Description
OntologyTerm	OntologyTerm.create(Entity entity)
static OntologyTerm	OntologyTerm.findById(Database db, Integer id)
static OntologyTerm	OntologyTerm.findByIdentifier(Database db, String identifier)
static OntologyTerm	OntologyTerm.findByOntologyTermAccession(Database db, Integer ontology, String termAccession)
OntologyTerm	Panel.getPanelType() Get the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).
OntologyTerm	Panel.getPanelType(Database db) Deprecated.

Methods in org.molgenis.omx.observ.target that return types with arguments of type OntologyTerm

Modifier and Type	Method and Description
static List<? extends OntologyTerm>	OntologyTerm.find(Database db, QueryRule... rules) Shorthand for db.find(OntologyTerm.class, org.molgenis.framework.db.QueryRule ...
static Query<? extends OntologyTerm>	OntologyTerm.query(Database db) Shorthand for db.query(OntologyTerm.class).

Methods in org.molgenis.omx.observ.target with parameters of type OntologyTerm

Modifier and Type	Method and Description
void	Panel.setPanelType(OntologyTerm panelType) Set the Indicate the type of Panel (example: Sample panel, AssayedPanel, Natural=wild type, Parental=parents of a cross, F1=First generation of cross, RCC=Recombinant congenic, CSS=chromosome substitution).

Constructors in org.molgenis.omx.observ.target with parameters of type OntologyTerm

Constructor and Description
OntologyTerm(OntologyTerm copyMe) copy constructor

Uses of OntologyTerm in org.molgenis.omx.observ.target.db

Classes in org.molgenis.omx.observ.target.db with type parameters of type OntologyTerm

Modifier and Type	Class and Description
class	OntologyTermSecurityDecorator<E extends OntologyTerm> TODO add column level security filters

Methods in org.molgenis.omx.observ.target.db that return OntologyTerm

Modifier and Type	Method and Description
OntologyTerm	OntologyTermJpaMapper.create()

Methods in org.molgenis.omx.observ.target.db that return types with arguments of type OntologyTerm

Modifier and Type	Method and Description
List<OntologyTerm>	OntologyTermJpaMapper.createList(int size) Return EMPTY list of given allocated size

Methods in org.molgenis.omx.observ.target.db with parameters of type OntologyTerm

Modifier and Type	Method and Description
void	OntologyTermJpaMapper.create(OntologyTerm entity) This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object
void	OntologyTermJpaMapper.destroy(OntologyTerm ontologyTerm)
void	OntologyTermJpaMapper.edit(OntologyTerm ontologyTerm)

Method parameters in org.molgenis.omx.observ.target.db with type arguments of type OntologyTerm

Modifier and Type	Method and Description
int	OntologyTermJpaMapper.executeAdd(List<? extends OntologyTerm> entities)
int	OntologyTermJpaMapper.executeRemove(List<? extends OntologyTerm> entities)
int	OntologyTermJpaMapper.executeUpdate(List<? extends OntologyTerm> entities)
void	OntologyTermJpaMapper.prepareFileAttachements(List<OntologyTerm> entities, File baseDir)
void	OntologyTermJpaMapper.resolveForeignKeys(List<OntologyTerm> entities)
boolean	OntologyTermJpaMapper.saveFileAttachements(List<OntologyTerm> entities, File baseDir)

Uses of OntologyTerm in org.molgenis.service

Methods in org.molgenis.service that return OntologyTerm

Modifier and Type	Method and Description
OntologyTerm	OntologyTermService.create(OntologyTerm ontologyTerm)
OntologyTerm	OntologyTermService.read(Integer id)

Methods in org.molgenis.service that return types with arguments of type OntologyTerm

Modifier and Type	Method and Description
Iterable<OntologyTerm>	OntologyTermService.readAll()
EntityPager<OntologyTerm>	OntologyTermService.readAll(int start, int num, List<QueryRule> queryRules)

Methods in org.molgenis.service with parameters of type OntologyTerm

Modifier and Type	Method and Description
OntologyTerm	OntologyTermService.create(OntologyTerm ontologyTerm)
void	OntologyTermService.update(OntologyTerm ontologyTerm)