Index (molgenis-omx-core 1.3.0 API)

A B C D E F G H I J L M N O P Q R S T U V X _

A

AbstractDataSetMatrixRepository - Class in org.molgenis.omx.dataset: Base class for DataSetMatrixRepository and OmxRepository
AbstractDataSetMatrixRepository(String, DataService, String) - Constructor for class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
Accession - Class in org.molgenis.omx.observ.target: Accession: An external identifier for an annotation.
Accession() - Constructor for class org.molgenis.omx.observ.target.Accession
AccessionMetaData - Class in org.molgenis.omx.observ.target
AccessionMetaData() - Constructor for class org.molgenis.omx.observ.target.AccessionMetaData
AccessionRepository - Class in org.molgenis.omx.observ.target
AccessionRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.AccessionRepository
AccessionRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.AccessionRepository: For testing purposes
ACTIVE - Static variable in class org.molgenis.omx.observ.Protocol
add(Iterable<? extends Entity>) - Method in class org.molgenis.omx.decorators.EmailValueDecorator
add(Entity) - Method in class org.molgenis.omx.decorators.EmailValueDecorator
add(Entity) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator
add(Iterable<? extends Entity>) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator
add(Entity) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
add(Iterable<? extends Entity>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
ADDRESS - Static variable in class org.molgenis.omx.auth.Institute
ADDRESS - Static variable in class org.molgenis.omx.auth.Person
AFFILIATION - Static variable in class org.molgenis.omx.auth.Person
afterPropertiesSet() - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
AsyncDataSetsIndexer - Class in org.molgenis.omx.search: Class that indexes all datasets for use in the dataexplorer async
AsyncDataSetsIndexer() - Constructor for class org.molgenis.omx.search.AsyncDataSetsIndexer
Autoid - Interface in org.molgenis.omx.core: Autoid: This interface assigns an automatic 'id'.
AUTOID - Static variable in class org.molgenis.omx.observ.ObservableFeature_Definitions
AUTOID - Static variable in class org.molgenis.omx.observ.Protocol_Features
AUTOID - Static variable in class org.molgenis.omx.observ.Protocol_RequiredFeatures
AUTOID - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols
AUTOID - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals
AUTOID - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value

B

BASE_URL - Static variable in class org.molgenis.omx.dataset.DataSetMatrixRepository
BASE_URL - Static variable in class org.molgenis.omx.protocol.CategoryRepository
BASE_URL - Static variable in class org.molgenis.omx.protocol.OmxLookupTableRepository
BASE_URL - Static variable in class org.molgenis.omx.protocol.ProtocolTreeRepository
BoolValue - Class in org.molgenis.omx.observ.value: BoolValue: .
BoolValue() - Constructor for class org.molgenis.omx.observ.value.BoolValue
BoolValueMetaData - Class in org.molgenis.omx.observ.value
BoolValueMetaData() - Constructor for class org.molgenis.omx.observ.value.BoolValueMetaData
BoolValueRepository - Class in org.molgenis.omx.observ.value
BoolValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.BoolValueRepository
BoolValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.BoolValueRepository: For testing purposes

C

CategoricalValue - Class in org.molgenis.omx.observ.value: CategoricalValue: .
CategoricalValue() - Constructor for class org.molgenis.omx.observ.value.CategoricalValue
CategoricalValueMetaData - Class in org.molgenis.omx.observ.value
CategoricalValueMetaData() - Constructor for class org.molgenis.omx.observ.value.CategoricalValueMetaData
CategoricalValueRepository - Class in org.molgenis.omx.observ.value
CategoricalValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.CategoricalValueRepository
CategoricalValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.CategoricalValueRepository: For testing purposes
Category - Class in org.molgenis.omx.observ: Category: Category is partOf ObservableFeature to define categories for an ObservableFeature, such as the categorical answer codes that are often used in Questionaires.
Category() - Constructor for class org.molgenis.omx.observ.Category
CategoryMetaData - Class in org.molgenis.omx.observ
CategoryMetaData() - Constructor for class org.molgenis.omx.observ.CategoryMetaData
CategoryRepository - Class in org.molgenis.omx.observ
CategoryRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.CategoryRepository
CategoryRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.CategoryRepository: For testing purposes
CategoryRepository - Class in org.molgenis.omx.protocol
CategoryRepository(Protocol, Integer, DataService) - Constructor for class org.molgenis.omx.protocol.CategoryRepository
Characteristic - Class in org.molgenis.omx.observ: Characteristic: Characteristics are yes-no statements about things in the world.
Characteristic() - Constructor for class org.molgenis.omx.observ.Characteristic
CharacteristicMetaData - Class in org.molgenis.omx.observ
CharacteristicMetaData() - Constructor for class org.molgenis.omx.observ.CharacteristicMetaData
CharacteristicRepository - Class in org.molgenis.omx.observ
CharacteristicRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.CharacteristicRepository
CharacteristicRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.CharacteristicRepository: For testing purposes
CITY - Static variable in class org.molgenis.omx.auth.Institute
CITY - Static variable in class org.molgenis.omx.auth.Person
CLASSNAME - Static variable in class org.molgenis.omx.core.MolgenisEntity
clearCache() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
close() - Method in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
close() - Method in class org.molgenis.omx.protocol.CategoryRepository
close() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
close() - Method in class org.molgenis.omx.protocol.ProtocolTreeRepository
closeTemplateSource(Object) - Method in class org.molgenis.omx.RepositoryTemplateLoader
ContactInterface - Interface in org.molgenis.omx.auth: ContactInterface: A contact is either a person or an organization.
count() - Method in class org.molgenis.omx.dataset.DataSetMatrixRepository
count() - Method in class org.molgenis.omx.protocol.CategoryRepository
count() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
count(Query) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
count() - Method in class org.molgenis.omx.protocol.ProtocolTreeRepository
COUNTRY - Static variable in class org.molgenis.omx.auth.Institute
COUNTRY - Static variable in class org.molgenis.omx.auth.Person
createOmxLookupTableEntityMetaDataName(String) - Static method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
CURRENTPANEL - Static variable in class org.molgenis.omx.observ.target.PanelSource

D

DataExplorerConfig - Class in org.molgenis.omx.config: Exposes the DataSetsIndexer and schedules dataset indexing 4 am every night
DataExplorerConfig() - Constructor for class org.molgenis.omx.config.DataExplorerConfig
dataService - Variable in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
DataSet - Class in org.molgenis.omx.observ: DataSet: Container for one or more observations that are measured using the same protocol and by the same performer(s).
DataSet() - Constructor for class org.molgenis.omx.observ.DataSet
DataSetDeleterController - Class in org.molgenis.omx.datasetdeleter
DataSetDeleterController(DataSetDeleterService, MolgenisSettings) - Constructor for class org.molgenis.omx.datasetdeleter.DataSetDeleterController
DataSetDeleterService - Interface in org.molgenis.omx.datasetdeleter
DataSetDeleterServiceImpl - Class in org.molgenis.omx.datasetdeleter
DataSetDeleterServiceImpl(DataService, SearchService) - Constructor for class org.molgenis.omx.datasetdeleter.DataSetDeleterServiceImpl
DataSetEntityMetaData - Class in org.molgenis.omx.dataset
DataSetEntityMetaData(DataSet) - Constructor for class org.molgenis.omx.dataset.DataSetEntityMetaData
dataSetIdentifier - Variable in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
DataSetMatrixRepository - Class in org.molgenis.omx.dataset: Repository around an omx DataSet matrix.
DataSetMatrixRepository(DataService, String) - Constructor for class org.molgenis.omx.dataset.DataSetMatrixRepository
DataSetMetaData - Class in org.molgenis.omx.observ
DataSetMetaData() - Constructor for class org.molgenis.omx.observ.DataSetMetaData
DataSetRepository - Class in org.molgenis.omx.observ
DataSetRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.DataSetRepository
DataSetRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.DataSetRepository: For testing purposes
dataSetsIndexer() - Method in class org.molgenis.omx.config.DataExplorerConfig: Get a reference to a DataSetsIndexer.
DataSetsIndexer - Interface in org.molgenis.omx.search: Indexes DataSet matrices.
DataSetsIndexerController - Class in org.molgenis.omx.controller: Controller class for the data explorer.
DataSetsIndexerController() - Constructor for class org.molgenis.omx.controller.DataSetsIndexerController
DataSetsIndexerStatusController - Class in org.molgenis.omx.controller: Controller class for the data explorer.
DataSetsIndexerStatusController() - Constructor for class org.molgenis.omx.controller.DataSetsIndexerStatusController
DATATYPE - Static variable in class org.molgenis.omx.observ.ObservableFeature
DateTimeValue - Class in org.molgenis.omx.observ.value: DateTimeValue: .
DateTimeValue() - Constructor for class org.molgenis.omx.observ.value.DateTimeValue
DateTimeValueMetaData - Class in org.molgenis.omx.observ.value
DateTimeValueMetaData() - Constructor for class org.molgenis.omx.observ.value.DateTimeValueMetaData
DateTimeValueRepository - Class in org.molgenis.omx.observ.value
DateTimeValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DateTimeValueRepository
DateTimeValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DateTimeValueRepository: For testing purposes
DateValue - Class in org.molgenis.omx.observ.value: DateValue: .
DateValue() - Constructor for class org.molgenis.omx.observ.value.DateValue
DateValueMetaData - Class in org.molgenis.omx.observ.value
DateValueMetaData() - Constructor for class org.molgenis.omx.observ.value.DateValueMetaData
DateValueRepository - Class in org.molgenis.omx.observ.value
DateValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DateValueRepository
DateValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DateValueRepository: For testing purposes
DecimalValue - Class in org.molgenis.omx.observ.value: DecimalValue: .
DecimalValue() - Constructor for class org.molgenis.omx.observ.value.DecimalValue
DecimalValueMetaData - Class in org.molgenis.omx.observ.value
DecimalValueMetaData() - Constructor for class org.molgenis.omx.observ.value.DecimalValueMetaData
DecimalValueRepository - Class in org.molgenis.omx.observ.value
DecimalValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DecimalValueRepository
DecimalValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.DecimalValueRepository: For testing purposes
DEFINITION - Static variable in class org.molgenis.omx.observ.Category
DEFINITION - Static variable in class org.molgenis.omx.observ.target.OntologyTerm
DEFINITIONS - Static variable in class org.molgenis.omx.observ.ObservableFeature
DEFINITIONS - Static variable in class org.molgenis.omx.observ.ObservableFeature_Definitions
delete(String, Boolean) - Method in class org.molgenis.omx.datasetdeleter.DataSetDeleterController
deleteData(String, boolean) - Method in interface org.molgenis.omx.datasetdeleter.DataSetDeleterService: Deletes data set data (DataSet, ObervationSets, ObservedValues, Values) and optionally data set meta data (Protocol, Category, ObservableFeature).
deleteData(String, boolean) - Method in class org.molgenis.omx.datasetdeleter.DataSetDeleterServiceImpl
deleteFileStorage(DataService) - Method in class org.molgenis.omx.services.StorageHandler: Remove file storage location and validation status.
DEPARTMENT - Static variable in class org.molgenis.omx.auth.Person
DESCRIPTION - Static variable in class org.molgenis.omx.observ.Characteristic

E

EMAIL - Static variable in class org.molgenis.omx.auth.Institute
EMAIL - Static variable in class org.molgenis.omx.auth.Person
EmailValue - Class in org.molgenis.omx.observ.value: EmailValue: .
EmailValue() - Constructor for class org.molgenis.omx.observ.value.EmailValue
EmailValueDecorator - Class in org.molgenis.omx.decorators
EmailValueDecorator(CrudRepository) - Constructor for class org.molgenis.omx.decorators.EmailValueDecorator
EmailValueMetaData - Class in org.molgenis.omx.observ.value
EmailValueMetaData() - Constructor for class org.molgenis.omx.observ.value.EmailValueMetaData
EmailValueRepository - Class in org.molgenis.omx.observ.value
EmailValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.EmailValueRepository
EmailValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.EmailValueRepository: For testing purposes
ENDTIME - Static variable in class org.molgenis.omx.observ.DataSet
ENTITY_ID_COLUMN_NAME - Static variable in class org.molgenis.omx.dataset.DataSetMatrixRepository
ENTITY_NAME - Static variable in class org.molgenis.omx.auth.Institute
ENTITY_NAME - Static variable in class org.molgenis.omx.auth.Person
ENTITY_NAME - Static variable in class org.molgenis.omx.auth.PersonRole
ENTITY_NAME - Static variable in class org.molgenis.omx.core.FreemarkerTemplate
ENTITY_NAME - Static variable in class org.molgenis.omx.core.MolgenisEntity
ENTITY_NAME - Static variable in class org.molgenis.omx.core.RuntimeProperty
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Category
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Characteristic
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.DataSet
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.ObservableFeature
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.ObservableFeature_Definitions
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.ObservationSet
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.ObservationTarget
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.ObservedValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Protocol
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Protocol_Features
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Protocol_RequiredFeatures
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Accession
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Individual
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Ontology
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.OntologyTerm
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Panel
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.PanelSource
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.target.Species
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.BoolValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.CategoricalValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.DateTimeValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.DateValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.DecimalValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.EmailValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.HtmlValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.HyperlinkValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.IntValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.LongValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.MrefValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.StringValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.TextValue
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.Value
ENTITY_NAME - Static variable in class org.molgenis.omx.observ.value.XrefValue
EntityToBoolValueConverter - Class in org.molgenis.omx.converters
EntityToBoolValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToBoolValueConverter
EntityToCategoricalValueConverter - Class in org.molgenis.omx.converters
EntityToCategoricalValueConverter(DataService) - Constructor for class org.molgenis.omx.converters.EntityToCategoricalValueConverter
EntityToDateTimeValueConverter - Class in org.molgenis.omx.converters
EntityToDateTimeValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToDateTimeValueConverter
EntityToDateValueConverter - Class in org.molgenis.omx.converters
EntityToDateValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToDateValueConverter
EntityToDecimalValueConverter - Class in org.molgenis.omx.converters
EntityToDecimalValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToDecimalValueConverter
EntityToEmailValueConverter - Class in org.molgenis.omx.converters
EntityToEmailValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToEmailValueConverter
EntityToHtmlValueConverter - Class in org.molgenis.omx.converters
EntityToHtmlValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToHtmlValueConverter
EntityToHyperlinkValueConverter - Class in org.molgenis.omx.converters
EntityToHyperlinkValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToHyperlinkValueConverter
EntityToIntValueConverter - Class in org.molgenis.omx.converters
EntityToIntValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToIntValueConverter
EntityToLongValueConverter - Class in org.molgenis.omx.converters
EntityToLongValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToLongValueConverter
EntityToMrefValueConverter - Class in org.molgenis.omx.converters
EntityToMrefValueConverter(CharacteristicLoadingCache) - Constructor for class org.molgenis.omx.converters.EntityToMrefValueConverter
EntityToStringValueConverter - Class in org.molgenis.omx.converters
EntityToStringValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToStringValueConverter
EntityToTextValueConverter - Class in org.molgenis.omx.converters
EntityToTextValueConverter() - Constructor for class org.molgenis.omx.converters.EntityToTextValueConverter
EntityToValueConverter<S extends Value,T> - Interface in org.molgenis.omx.converters
EntityToXrefValueConverter - Class in org.molgenis.omx.converters
EntityToXrefValueConverter(CharacteristicLoadingCache) - Constructor for class org.molgenis.omx.converters.EntityToXrefValueConverter
equals(Object) - Method in class org.molgenis.omx.auth.Institute
equals(Object) - Method in class org.molgenis.omx.auth.Person
equals(Object) - Method in class org.molgenis.omx.auth.PersonRole
equals(Object) - Method in class org.molgenis.omx.core.FreemarkerTemplate
equals(Object) - Method in class org.molgenis.omx.core.MolgenisEntity
equals(Object) - Method in class org.molgenis.omx.core.RuntimeProperty
equals(Object) - Method in class org.molgenis.omx.observ.Category
equals(Object) - Method in class org.molgenis.omx.observ.Characteristic
equals(Object) - Method in class org.molgenis.omx.observ.DataSet
equals(Object) - Method in class org.molgenis.omx.observ.ObservableFeature
equals(Object) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
equals(Object) - Method in class org.molgenis.omx.observ.ObservationSet
equals(Object) - Method in class org.molgenis.omx.observ.ObservationTarget
equals(Object) - Method in class org.molgenis.omx.observ.ObservedValue
equals(Object) - Method in class org.molgenis.omx.observ.Protocol
equals(Object) - Method in class org.molgenis.omx.observ.Protocol_Features
equals(Object) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
equals(Object) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
equals(Object) - Method in class org.molgenis.omx.observ.target.Accession
equals(Object) - Method in class org.molgenis.omx.observ.target.Individual
equals(Object) - Method in class org.molgenis.omx.observ.target.Ontology
equals(Object) - Method in class org.molgenis.omx.observ.target.OntologyTerm
equals(Object) - Method in class org.molgenis.omx.observ.target.Panel
equals(Object) - Method in class org.molgenis.omx.observ.target.Panel_Individuals
equals(Object) - Method in class org.molgenis.omx.observ.target.PanelSource
equals(Object) - Method in class org.molgenis.omx.observ.target.Species
equals(Object) - Method in class org.molgenis.omx.observ.value.BoolValue
equals(Object) - Method in class org.molgenis.omx.observ.value.CategoricalValue
equals(Object) - Method in class org.molgenis.omx.observ.value.DateTimeValue
equals(Object) - Method in class org.molgenis.omx.observ.value.DateValue
equals(Object) - Method in class org.molgenis.omx.observ.value.DecimalValue
equals(Object) - Method in class org.molgenis.omx.observ.value.EmailValue
equals(Object) - Method in class org.molgenis.omx.observ.value.HtmlValue
equals(Object) - Method in class org.molgenis.omx.observ.value.HyperlinkValue
equals(Object) - Method in class org.molgenis.omx.observ.value.IntValue
equals(Object) - Method in class org.molgenis.omx.observ.value.LongValue
equals(Object) - Method in class org.molgenis.omx.observ.value.MrefValue
equals(Object) - Method in class org.molgenis.omx.observ.value.MrefValue_Value
equals(Object) - Method in class org.molgenis.omx.observ.value.StringValue
equals(Object) - Method in class org.molgenis.omx.observ.value.TextValue
equals(Object) - Method in class org.molgenis.omx.observ.value.Value
equals(Object) - Method in class org.molgenis.omx.observ.value.XrefValue
equals(Object) - Method in class org.molgenis.omx.RepositoryTemplateLoader.TemplateSource
equals(Object) - Method in class org.molgenis.omx.utils.ValueCell
escapeEntityNameStrict(String) - Static method in class org.molgenis.omx.decorators.NameConvention: Converts an entity name into its safe version, so that they can be used in contexts such as programming environments where strict names are needed.
escapeFileName(String) - Static method in class org.molgenis.omx.decorators.NameConvention: Converts file name into its safe version, so that they can be safely stored on any file system.

F

FATHER - Static variable in class org.molgenis.omx.observ.target.Individual
FAX - Static variable in class org.molgenis.omx.auth.Institute
FAX - Static variable in class org.molgenis.omx.auth.Person
FEATURE - Static variable in class org.molgenis.omx.observ.ObservedValue
FEATURES - Static variable in class org.molgenis.omx.observ.Protocol
FEATURES - Static variable in class org.molgenis.omx.observ.Protocol_Features
findAll(Query) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findAll(Query, Class<E>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findAll(Iterable<Object>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findAll(Iterable<Object>, Class<E>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findOne(Query) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findOne(Object) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findOne(Object, Class<E>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findOne(Query, Class<E>) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
findTemplateSource(String) - Method in class org.molgenis.omx.RepositoryTemplateLoader
FIRSTNAME - Static variable in class org.molgenis.omx.auth.Person
flush() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
FreemarkerTemplate - Class in org.molgenis.omx.core: FreemarkerTemplate: .
FreemarkerTemplate() - Constructor for class org.molgenis.omx.core.FreemarkerTemplate
FreemarkerTemplateMetaData - Class in org.molgenis.omx.core
FreemarkerTemplateMetaData() - Constructor for class org.molgenis.omx.core.FreemarkerTemplateMetaData
FreemarkerTemplateRepository - Class in org.molgenis.omx.core
FreemarkerTemplateRepository(QueryResolver) - Constructor for class org.molgenis.omx.core.FreemarkerTemplateRepository
FreemarkerTemplateRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.core.FreemarkerTemplateRepository: For testing purposes
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToBoolValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToCategoricalValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDateTimeValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDateValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDecimalValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToEmailValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToHtmlValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToHyperlinkValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToIntValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToLongValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToMrefValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToStringValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToTextValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in interface org.molgenis.omx.converters.EntityToValueConverter: Converts an entity column value to a value entity
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToXrefValueConverter
fromEntity(Entity, String, ObservableFeature) - Method in class org.molgenis.omx.converters.ValueConverter

G

get(String) - Method in class org.molgenis.omx.auth.Institute: Generic getter.
get(String) - Method in class org.molgenis.omx.auth.Person: Generic getter.
get(String) - Method in class org.molgenis.omx.auth.PersonRole: Generic getter.
get(String) - Method in class org.molgenis.omx.core.FreemarkerTemplate: Generic getter.
get(String) - Method in class org.molgenis.omx.core.MolgenisEntity: Generic getter.
get(String) - Method in class org.molgenis.omx.core.RuntimeProperty: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Category: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Characteristic: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.DataSet: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.ObservableFeature: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.ObservationSet: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.ObservationTarget: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.ObservedValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Protocol: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Protocol_Features: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Accession: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Individual: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Ontology: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Panel: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.PanelSource: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.target.Species: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.BoolValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.CategoricalValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.DateTimeValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.DateValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.DecimalValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.EmailValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.HtmlValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.IntValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.LongValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.MrefValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.StringValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.TextValue: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.Value: Generic getter.
get(String) - Method in class org.molgenis.omx.observ.value.XrefValue: Generic getter.
get(String) - Static method in class org.molgenis.omx.utils.I18nTools: If the given string is a internationalized string return the value for the default language, else return the input string
get(String, String) - Static method in class org.molgenis.omx.utils.I18nTools: If the given string is a internationalized string return the value for the given languange, else return the input string
get__Type() - Method in class org.molgenis.omx.observ.Characteristic: Get the Subtypes have to be set to allow searching.
get__Type() - Method in class org.molgenis.omx.observ.value.Value: Get the Subtypes have to be set to allow searching.
get__TypeLabel() - Method in class org.molgenis.omx.observ.Characteristic: Get tha label for enum __Type.
get__TypeLabel() - Method in class org.molgenis.omx.observ.value.Value: Get tha label for enum __Type.
get__TypeOptions() - Method in class org.molgenis.omx.observ.Characteristic: __Type is enum.
get__TypeOptions() - Method in class org.molgenis.omx.observ.value.Value: __Type is enum.
getActive() - Method in class org.molgenis.omx.observ.Protocol: Get the whether this protocol is considered active/inactive.
getAddress() - Method in interface org.molgenis.omx.auth.ContactInterface
getAddress() - Method in class org.molgenis.omx.auth.Institute: Get the The address of the Contact..
getAddress() - Method in class org.molgenis.omx.auth.Person: Get the The address of the Contact..
getAddress() - Method in interface org.molgenis.omx.auth.PersonInterface
getAffiliation() - Method in class org.molgenis.omx.auth.Person: Get the .
getAffiliation() - Method in interface org.molgenis.omx.auth.PersonInterface
getAtomicAttributes() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getAttributeNames() - Method in class org.molgenis.omx.auth.Institute
getAttributeNames() - Method in class org.molgenis.omx.auth.Person
getAttributeNames() - Method in class org.molgenis.omx.auth.PersonRole
getAttributeNames() - Method in class org.molgenis.omx.core.FreemarkerTemplate
getAttributeNames() - Method in class org.molgenis.omx.core.MolgenisEntity
getAttributeNames() - Method in class org.molgenis.omx.core.RuntimeProperty
getAttributeNames() - Method in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
getAttributeNames() - Method in class org.molgenis.omx.observ.Category
getAttributeNames() - Method in class org.molgenis.omx.observ.Characteristic
getAttributeNames() - Method in class org.molgenis.omx.observ.DataSet
getAttributeNames() - Method in class org.molgenis.omx.observ.ObservableFeature
getAttributeNames() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
getAttributeNames() - Method in class org.molgenis.omx.observ.ObservationSet
getAttributeNames() - Method in class org.molgenis.omx.observ.ObservationTarget
getAttributeNames() - Method in class org.molgenis.omx.observ.ObservedValue
getAttributeNames() - Method in class org.molgenis.omx.observ.Protocol
getAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_Features
getAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
getAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Accession
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Individual
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Ontology
getAttributeNames() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Panel
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
getAttributeNames() - Method in class org.molgenis.omx.observ.target.PanelSource
getAttributeNames() - Method in class org.molgenis.omx.observ.target.Species
getAttributeNames() - Method in class org.molgenis.omx.observ.value.BoolValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.CategoricalValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.DateTimeValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.DateValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.DecimalValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.EmailValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.HtmlValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.IntValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.LongValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.MrefValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
getAttributeNames() - Method in class org.molgenis.omx.observ.value.StringValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.TextValue
getAttributeNames() - Method in class org.molgenis.omx.observ.value.Value
getAttributeNames() - Method in class org.molgenis.omx.observ.value.XrefValue
getAttributeParts() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getAttributeParts() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getAttributes() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getAttributes() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getAttributes() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getAutoid() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.observ.Protocol_Features: Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Get the automatic id field to ensure ordering of mrefs.
getBooleanProperty(String) - Method in class org.molgenis.omx.MolgenisDbSettings
getBooleanProperty(String, boolean) - Method in class org.molgenis.omx.MolgenisDbSettings
getCity() - Method in interface org.molgenis.omx.auth.ContactInterface
getCity() - Method in class org.molgenis.omx.auth.Institute: Get the Added from the old definition of MolgenisUser.
getCity() - Method in class org.molgenis.omx.auth.Person: Get the Added from the old definition of MolgenisUser.
getCity() - Method in interface org.molgenis.omx.auth.PersonInterface
getClassName() - Method in class org.molgenis.omx.core.MolgenisEntity: Get the Full name of the entity.
getCountry() - Method in interface org.molgenis.omx.auth.ContactInterface
getCountry() - Method in class org.molgenis.omx.auth.Institute: Get the Added from the old definition of MolgenisUser.
getCountry() - Method in class org.molgenis.omx.auth.Person: Get the Added from the old definition of MolgenisUser.
getCountry() - Method in interface org.molgenis.omx.auth.PersonInterface
getCurrentPanel() - Method in class org.molgenis.omx.observ.target.PanelSource: Get the Panel for which these sources are defined..
getDataSet() - Method in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
getDataType() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the (Optional) Reference to the technical data type.
getDataType() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getDataType() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getDataTypeLabel() - Method in class org.molgenis.omx.observ.ObservableFeature: Get tha label for enum DataType.
getDataTypeOptions() - Method in class org.molgenis.omx.observ.ObservableFeature: DataType is enum.
getDefaultValue() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getDefaultValue() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getDefinition() - Method in class org.molgenis.omx.observ.Category: Get the The category that is being measured in a specific way..
getDefinition() - Method in class org.molgenis.omx.observ.target.OntologyTerm: Get the (Optional) The definition of the term..
getDefinitions() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the The concept that is being measured in a specific way..
getDefinitions() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Get the .
getDefinitionsObservableFeatureCollection() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getDepartment() - Method in class org.molgenis.omx.auth.Person: Get the Added from the old definition of MolgenisUser.
getDepartment() - Method in interface org.molgenis.omx.auth.PersonInterface
getDescription() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getDescription() - Method in class org.molgenis.omx.observ.Characteristic: Get the (Optional) Rudimentary meta data about the observable feature.
getDescription() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getDescription() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getDescription() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getDescription() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getEmail() - Method in interface org.molgenis.omx.auth.ContactInterface
getEmail() - Method in class org.molgenis.omx.auth.Institute: Get the The email address of the Contact..
getEmail() - Method in class org.molgenis.omx.auth.Person: Get the The email address of the Contact..
getEmail() - Method in interface org.molgenis.omx.auth.PersonInterface
getEndTime() - Method in class org.molgenis.omx.observ.DataSet: Get the (Optional) time when the protocol ended..
getEntityClass() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getEntityClass() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getEntityClass() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getEntityMetaData() - Method in class org.molgenis.omx.auth.Institute
getEntityMetaData() - Method in class org.molgenis.omx.auth.Person
getEntityMetaData() - Method in class org.molgenis.omx.auth.PersonRole
getEntityMetaData() - Method in class org.molgenis.omx.core.FreemarkerTemplate
getEntityMetaData() - Method in class org.molgenis.omx.core.MolgenisEntity
getEntityMetaData() - Method in class org.molgenis.omx.core.RuntimeProperty
getEntityMetaData() - Method in class org.molgenis.omx.dataset.AbstractDataSetMatrixRepository
getEntityMetaData() - Method in class org.molgenis.omx.observ.Category
getEntityMetaData() - Method in class org.molgenis.omx.observ.Characteristic
getEntityMetaData() - Method in class org.molgenis.omx.observ.DataSet
getEntityMetaData() - Method in class org.molgenis.omx.observ.ObservableFeature
getEntityMetaData() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
getEntityMetaData() - Method in class org.molgenis.omx.observ.ObservationSet
getEntityMetaData() - Method in class org.molgenis.omx.observ.ObservationTarget
getEntityMetaData() - Method in class org.molgenis.omx.observ.ObservedValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.Protocol
getEntityMetaData() - Method in class org.molgenis.omx.observ.Protocol_Features
getEntityMetaData() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
getEntityMetaData() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Accession
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Individual
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Ontology
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Panel
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.PanelSource
getEntityMetaData() - Method in class org.molgenis.omx.observ.target.Species
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.BoolValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.CategoricalValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.DateTimeValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.DateValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.DecimalValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.EmailValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.HtmlValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.IntValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.LongValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.MrefValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.StringValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.TextValue
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.Value
getEntityMetaData() - Method in class org.molgenis.omx.observ.value.XrefValue
getEntityMetaData() - Method in class org.molgenis.omx.protocol.CategoryRepository
getEntityMetaData() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
getEntityMetaData() - Method in class org.molgenis.omx.protocol.ProtocolTreeRepository
getEntityName() - Method in class org.molgenis.omx.auth.Institute
getEntityName() - Method in class org.molgenis.omx.auth.Person
getEntityName() - Method in class org.molgenis.omx.auth.PersonRole
getEntityName() - Method in class org.molgenis.omx.core.FreemarkerTemplate
getEntityName() - Method in class org.molgenis.omx.core.MolgenisEntity
getEntityName() - Method in class org.molgenis.omx.core.RuntimeProperty
getEntityName() - Method in class org.molgenis.omx.observ.Category
getEntityName() - Method in class org.molgenis.omx.observ.Characteristic
getEntityName() - Method in class org.molgenis.omx.observ.DataSet
getEntityName() - Method in class org.molgenis.omx.observ.ObservableFeature
getEntityName() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
getEntityName() - Method in class org.molgenis.omx.observ.ObservationSet
getEntityName() - Method in class org.molgenis.omx.observ.ObservationTarget
getEntityName() - Method in class org.molgenis.omx.observ.ObservedValue
getEntityName() - Method in class org.molgenis.omx.observ.Protocol
getEntityName() - Method in class org.molgenis.omx.observ.Protocol_Features
getEntityName() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
getEntityName() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
getEntityName() - Method in class org.molgenis.omx.observ.target.Accession
getEntityName() - Method in class org.molgenis.omx.observ.target.Individual
getEntityName() - Method in class org.molgenis.omx.observ.target.Ontology
getEntityName() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getEntityName() - Method in class org.molgenis.omx.observ.target.Panel
getEntityName() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
getEntityName() - Method in class org.molgenis.omx.observ.target.PanelSource
getEntityName() - Method in class org.molgenis.omx.observ.target.Species
getEntityName() - Method in class org.molgenis.omx.observ.value.BoolValue
getEntityName() - Method in class org.molgenis.omx.observ.value.CategoricalValue
getEntityName() - Method in class org.molgenis.omx.observ.value.DateTimeValue
getEntityName() - Method in class org.molgenis.omx.observ.value.DateValue
getEntityName() - Method in class org.molgenis.omx.observ.value.DecimalValue
getEntityName() - Method in class org.molgenis.omx.observ.value.EmailValue
getEntityName() - Method in class org.molgenis.omx.observ.value.HtmlValue
getEntityName() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
getEntityName() - Method in class org.molgenis.omx.observ.value.IntValue
getEntityName() - Method in class org.molgenis.omx.observ.value.LongValue
getEntityName() - Method in class org.molgenis.omx.observ.value.MrefValue
getEntityName() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
getEntityName() - Method in class org.molgenis.omx.observ.value.StringValue
getEntityName() - Method in class org.molgenis.omx.observ.value.TextValue
getEntityName() - Method in class org.molgenis.omx.observ.value.Value
getEntityName() - Method in class org.molgenis.omx.observ.value.XrefValue
getEnumOptions() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getEnumOptions() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getExtends() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getExtends() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getExtends() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getFather() - Method in class org.molgenis.omx.observ.target.Individual: Get the Refers to the father of the individual..
getFax() - Method in interface org.molgenis.omx.auth.ContactInterface
getFax() - Method in class org.molgenis.omx.auth.Institute: Get the The fax number of the Contact..
getFax() - Method in class org.molgenis.omx.auth.Person: Get the The fax number of the Contact..
getFax() - Method in interface org.molgenis.omx.auth.PersonInterface
getFeature() - Method in class org.molgenis.omx.observ.ObservedValue: Get the References the ObservableFeature that this observation was made on.
getFeatures() - Method in class org.molgenis.omx.observ.Protocol: Get the parameters (in/out) that are used or produced by this protocol..
getFeatures() - Method in class org.molgenis.omx.observ.Protocol_Features: Get the .
getFeaturesProtocolCollection() - Method in class org.molgenis.omx.observ.ObservableFeature
getFileStorage() - Method in class org.molgenis.omx.services.Report
getFileStorage(DataService) - Method in class org.molgenis.omx.services.StorageHandler: Get the path of the file storage, regardless whether it is valid or not.
getFileStorage(boolean, DataService) - Method in class org.molgenis.omx.services.StorageHandler: Get the path of the file storage.
getFileStoragePropsPresent() - Method in class org.molgenis.omx.services.Report
getFirstName() - Method in class org.molgenis.omx.auth.Person: Get the .
getFirstName() - Method in interface org.molgenis.omx.auth.PersonInterface
getFolderExists() - Method in class org.molgenis.omx.services.Report
getFolderHasContent() - Method in class org.molgenis.omx.services.Report
getId() - Method in interface org.molgenis.omx.core.Autoid
getId() - Method in class org.molgenis.omx.core.FreemarkerTemplate: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.core.MolgenisEntity: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.core.RuntimeProperty: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.Characteristic: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.ObservationSet: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.ObservedValue: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.target.Ontology: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.target.PanelSource: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.observ.value.Value: Get the automatically generated internal id, only for internal use..
getId() - Method in class org.molgenis.omx.utils.ValueCell
getIdentifier() - Method in interface org.molgenis.omx.core.Identifiable
getIdentifier() - Method in class org.molgenis.omx.core.RuntimeProperty: Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
getIdentifier() - Method in class org.molgenis.omx.observ.Characteristic: Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
getIdentifier() - Method in class org.molgenis.omx.observ.ObservationSet: Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
getIdentifier() - Method in class org.molgenis.omx.observ.target.Ontology: Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
getIdValue() - Method in class org.molgenis.omx.auth.Institute
getIdValue() - Method in class org.molgenis.omx.auth.Person
getIdValue() - Method in class org.molgenis.omx.auth.PersonRole
getIdValue() - Method in class org.molgenis.omx.core.FreemarkerTemplate
getIdValue() - Method in class org.molgenis.omx.core.MolgenisEntity
getIdValue() - Method in class org.molgenis.omx.core.RuntimeProperty
getIdValue() - Method in class org.molgenis.omx.observ.Category
getIdValue() - Method in class org.molgenis.omx.observ.Characteristic
getIdValue() - Method in class org.molgenis.omx.observ.DataSet
getIdValue() - Method in class org.molgenis.omx.observ.ObservableFeature
getIdValue() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
getIdValue() - Method in class org.molgenis.omx.observ.ObservationSet
getIdValue() - Method in class org.molgenis.omx.observ.ObservationTarget
getIdValue() - Method in class org.molgenis.omx.observ.ObservedValue
getIdValue() - Method in class org.molgenis.omx.observ.Protocol
getIdValue() - Method in class org.molgenis.omx.observ.Protocol_Features
getIdValue() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
getIdValue() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
getIdValue() - Method in class org.molgenis.omx.observ.target.Accession
getIdValue() - Method in class org.molgenis.omx.observ.target.Individual
getIdValue() - Method in class org.molgenis.omx.observ.target.Ontology
getIdValue() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getIdValue() - Method in class org.molgenis.omx.observ.target.Panel
getIdValue() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
getIdValue() - Method in class org.molgenis.omx.observ.target.PanelSource
getIdValue() - Method in class org.molgenis.omx.observ.target.Species
getIdValue() - Method in class org.molgenis.omx.observ.value.BoolValue
getIdValue() - Method in class org.molgenis.omx.observ.value.CategoricalValue
getIdValue() - Method in class org.molgenis.omx.observ.value.DateTimeValue
getIdValue() - Method in class org.molgenis.omx.observ.value.DateValue
getIdValue() - Method in class org.molgenis.omx.observ.value.DecimalValue
getIdValue() - Method in class org.molgenis.omx.observ.value.EmailValue
getIdValue() - Method in class org.molgenis.omx.observ.value.HtmlValue
getIdValue() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
getIdValue() - Method in class org.molgenis.omx.observ.value.IntValue
getIdValue() - Method in class org.molgenis.omx.observ.value.LongValue
getIdValue() - Method in class org.molgenis.omx.observ.value.MrefValue
getIdValue() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
getIdValue() - Method in class org.molgenis.omx.observ.value.StringValue
getIdValue() - Method in class org.molgenis.omx.observ.value.TextValue
getIdValue() - Method in class org.molgenis.omx.observ.value.Value
getIdValue() - Method in class org.molgenis.omx.observ.value.XrefValue
getIndividuals() - Method in class org.molgenis.omx.observ.target.Panel: Get the The list of individuals in this panel.
getIndividuals() - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Get the .
getIndividualsPanelCollection() - Method in class org.molgenis.omx.observ.target.Individual
getIntegerProperty(String) - Method in class org.molgenis.omx.MolgenisDbSettings
getIsMissing() - Method in class org.molgenis.omx.observ.Category: Get the whether this value should be treated as missing value..
getKey() - Method in class org.molgenis.omx.utils.ValueCell
getLabel() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getLabel() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getLabel() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getLabel() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getLabel() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getLabelAttributeNames() - Method in class org.molgenis.omx.auth.Institute
getLabelAttributeNames() - Method in class org.molgenis.omx.auth.Person
getLabelAttributeNames() - Method in class org.molgenis.omx.auth.PersonRole
getLabelAttributeNames() - Method in class org.molgenis.omx.core.FreemarkerTemplate
getLabelAttributeNames() - Method in class org.molgenis.omx.core.MolgenisEntity
getLabelAttributeNames() - Method in class org.molgenis.omx.core.RuntimeProperty
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Category
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Characteristic
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.DataSet
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.ObservableFeature
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.ObservationSet
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.ObservationTarget
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.ObservedValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Protocol
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_Features
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Accession
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Individual
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Ontology
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.OntologyTerm
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Panel
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.PanelSource
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.target.Species
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.BoolValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.CategoricalValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.DateTimeValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.DateValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.DecimalValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.EmailValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.HtmlValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.IntValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.LongValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.MrefValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.StringValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.TextValue
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.Value
getLabelAttributeNames() - Method in class org.molgenis.omx.observ.value.XrefValue
getLastModified(Object) - Method in class org.molgenis.omx.RepositoryTemplateLoader: The repository does not offer a way to check last modified date.
getLastName() - Method in class org.molgenis.omx.auth.Person: Get the .
getLastName() - Method in interface org.molgenis.omx.auth.PersonInterface
getMaxRange() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the for numeric values this is used to set the 'max' value of the slider user interface.
getMidInitials() - Method in class org.molgenis.omx.auth.Person: Get the .
getMidInitials() - Method in interface org.molgenis.omx.auth.PersonInterface
getMinRange() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the for numeric values this is used to set the 'min' value of the slider user interface.
getMother() - Method in class org.molgenis.omx.observ.target.Individual: Get the Refers to the mother of the individual..
getMrefValue() - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Get the .
getName() - Method in class org.molgenis.omx.auth.Institute: Get the .
getName() - Method in class org.molgenis.omx.core.FreemarkerTemplate: Get the Name of the entity.
getName() - Method in interface org.molgenis.omx.core.Identifiable
getName() - Method in class org.molgenis.omx.core.MolgenisEntity: Get the Name of the entity.
getName() - Method in class org.molgenis.omx.core.RuntimeProperty: Get the human readible name, not necessary unique..
getName() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getName() - Method in class org.molgenis.omx.observ.Characteristic: Get the human readible name, not necessary unique..
getName() - Method in class org.molgenis.omx.observ.target.Ontology: Get the human readible name, not necessary unique..
getName() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getName() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getName() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getName() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getNumberOfIndividuals() - Method in class org.molgenis.omx.observ.target.Panel: Get the .
getNumberOfIndividuals() - Method in class org.molgenis.omx.observ.target.PanelSource: Get the Number of individuals lifted over from this source.
getObservableFeature() - Method in class org.molgenis.omx.observ.Category: Get the The Measurement these permitted values are part of..
getObservableFeature() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Get the .
getObservationSet() - Method in class org.molgenis.omx.observ.ObservedValue: Get the Reference to the observation.
getOntology() - Method in class org.molgenis.omx.observ.target.OntologyTerm: Get the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
getOntologyAccession() - Method in class org.molgenis.omx.observ.target.Ontology: Get the A accession that uniquely identifies the ontology (typically an acronym).
getOntologyURI() - Method in class org.molgenis.omx.observ.target.Ontology: Get the (Optional) A URI that references the location of the ontology..
getOrder() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepositoryRegistrator
getPackage() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getPackage() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getPackage() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getPanel() - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Get the .
getPanelType() - Method in class org.molgenis.omx.observ.target.Panel: 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).
getPartOfDataSet() - Method in class org.molgenis.omx.observ.ObservationSet: Get the DataSet this ValueSet is part of..
getPhone() - Method in interface org.molgenis.omx.auth.ContactInterface
getPhone() - Method in class org.molgenis.omx.auth.Institute: Get the The telephone number of the Contact including the suitable area codes..
getPhone() - Method in class org.molgenis.omx.auth.Person: Get the The telephone number of the Contact including the suitable area codes..
getPhone() - Method in interface org.molgenis.omx.auth.PersonInterface
getProperties(String) - Method in class org.molgenis.omx.MolgenisDbSettings
getProperty(String) - Method in class org.molgenis.omx.MolgenisDbSettings
getProperty(String, String) - Method in class org.molgenis.omx.MolgenisDbSettings
getProtocol() - Method in class org.molgenis.omx.observ.Protocol_Features: Get the .
getProtocol() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Get the .
getProtocol() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Get the .
getProtocolDescendants(Protocol) - Static method in class org.molgenis.omx.utils.ProtocolUtils: Returns the descendants of the given protocol including the given protocol
getProtocolDescendants(Protocol, boolean) - Static method in class org.molgenis.omx.utils.ProtocolUtils: Returns the descendants of the given protocol
getProtocolType() - Method in class org.molgenis.omx.observ.Protocol: Get the classification of protocol.
getProtocolUsed() - Method in class org.molgenis.omx.observ.DataSet: Get the Reference to the protocol that is being used (if available).
getRange() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getRange() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getReader(Object, String) - Method in class org.molgenis.omx.RepositoryTemplateLoader
getRefEntity() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
getRefEntity() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
getReport() - Method in class org.molgenis.omx.services.StorageHandler
getRequiredFeatures() - Method in class org.molgenis.omx.observ.Protocol: Get the ...........
getRequiredFeatures() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Get the .
getRequiredFeaturesProtocolCollection() - Method in class org.molgenis.omx.observ.ObservableFeature
getRoles() - Method in class org.molgenis.omx.auth.Person: Get the Indicate role of the contact, e.g.
getRoles() - Method in interface org.molgenis.omx.auth.PersonInterface
getRoot() - Method in class org.molgenis.omx.observ.Protocol: Get the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..
getSelectionCriteria() - Method in class org.molgenis.omx.observ.target.PanelSource: Get the Inclusion/exclusion criteria used to select these individuals from source into current panel.
getSimpleName() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
getSimpleName() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
getSimpleName() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
getSourcePanel() - Method in class org.molgenis.omx.observ.target.PanelSource: Get the Source that contributed individuals to current panel.
getSpecies() - Method in class org.molgenis.omx.observ.target.Panel: Get the The species this panel is an instance of/part of/extracted from..
getStartTime() - Method in class org.molgenis.omx.observ.DataSet: Get the time when the protocol started..
getSubprotocols() - Method in class org.molgenis.omx.observ.Protocol: Get the Subprotocols of this protocol.
getSubprotocols() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Get the .
getSubprotocolsProtocolCollection() - Method in class org.molgenis.omx.observ.Protocol
getTemporal() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the Whether this feature is time dependent and can have different values when measured on different times (e.g.
getTermAccession() - Method in class org.molgenis.omx.observ.target.OntologyTerm: Get the (Optional) The accession number assigned to the ontology term in its source ontology.
getTime() - Method in class org.molgenis.omx.observ.ObservationSet: Get the Time of this observationSet.
getTitle() - Method in class org.molgenis.omx.auth.Person: Get the An academic title, e.g.
getTitle() - Method in interface org.molgenis.omx.auth.PersonInterface
getTollFreePhone() - Method in interface org.molgenis.omx.auth.ContactInterface
getTollFreePhone() - Method in class org.molgenis.omx.auth.Institute: Get the A toll free phone number for the Contact, including suitable area codes..
getTollFreePhone() - Method in class org.molgenis.omx.auth.Person: Get the A toll free phone number for the Contact, including suitable area codes..
getTollFreePhone() - Method in interface org.molgenis.omx.auth.PersonInterface
getType() - Method in class org.molgenis.omx.core.MolgenisEntity: Get the Type of the entity.
getUnit() - Method in class org.molgenis.omx.observ.ObservableFeature: Get the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).
getValue() - Method in class org.molgenis.omx.core.FreemarkerTemplate: Get the .
getValue() - Method in class org.molgenis.omx.core.RuntimeProperty: Get the .
getValue() - Method in class org.molgenis.omx.observ.ObservedValue: Get the The value observed.
getValue() - Method in class org.molgenis.omx.observ.value.BoolValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.CategoricalValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.DateTimeValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.DateValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.DecimalValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.EmailValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.HtmlValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.HyperlinkValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.IntValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.LongValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.MrefValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.StringValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.TextValue: Get the .
getValue() - Method in class org.molgenis.omx.observ.value.XrefValue: Get the .
getValue() - Method in class org.molgenis.omx.utils.ValueCell
getValueCode() - Method in class org.molgenis.omx.observ.Category: Get the The value used to store this category in ObservedValue.
getValueMrefValueCollection() - Method in class org.molgenis.omx.observ.Characteristic
getVerified() - Method in class org.molgenis.omx.services.Report

H

handleRuntimeException(RuntimeException) - Method in class org.molgenis.omx.datasetdeleter.DataSetDeleterController
hasFileStorage(boolean, DataService) - Method in class org.molgenis.omx.services.StorageHandler: Ask if these is a file storage location available, regardless whether it is valid or not.
hashCode() - Method in class org.molgenis.omx.auth.Institute
hashCode() - Method in class org.molgenis.omx.auth.Person
hashCode() - Method in class org.molgenis.omx.auth.PersonRole
hashCode() - Method in class org.molgenis.omx.core.FreemarkerTemplate
hashCode() - Method in class org.molgenis.omx.core.MolgenisEntity
hashCode() - Method in class org.molgenis.omx.core.RuntimeProperty
hashCode() - Method in class org.molgenis.omx.observ.Category
hashCode() - Method in class org.molgenis.omx.observ.Characteristic
hashCode() - Method in class org.molgenis.omx.observ.DataSet
hashCode() - Method in class org.molgenis.omx.observ.ObservableFeature
hashCode() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
hashCode() - Method in class org.molgenis.omx.observ.ObservationSet
hashCode() - Method in class org.molgenis.omx.observ.ObservationTarget
hashCode() - Method in class org.molgenis.omx.observ.ObservedValue
hashCode() - Method in class org.molgenis.omx.observ.Protocol
hashCode() - Method in class org.molgenis.omx.observ.Protocol_Features
hashCode() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
hashCode() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
hashCode() - Method in class org.molgenis.omx.observ.target.Accession
hashCode() - Method in class org.molgenis.omx.observ.target.Individual
hashCode() - Method in class org.molgenis.omx.observ.target.Ontology
hashCode() - Method in class org.molgenis.omx.observ.target.OntologyTerm
hashCode() - Method in class org.molgenis.omx.observ.target.Panel
hashCode() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
hashCode() - Method in class org.molgenis.omx.observ.target.PanelSource
hashCode() - Method in class org.molgenis.omx.observ.target.Species
hashCode() - Method in class org.molgenis.omx.observ.value.BoolValue
hashCode() - Method in class org.molgenis.omx.observ.value.CategoricalValue
hashCode() - Method in class org.molgenis.omx.observ.value.DateTimeValue
hashCode() - Method in class org.molgenis.omx.observ.value.DateValue
hashCode() - Method in class org.molgenis.omx.observ.value.DecimalValue
hashCode() - Method in class org.molgenis.omx.observ.value.EmailValue
hashCode() - Method in class org.molgenis.omx.observ.value.HtmlValue
hashCode() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
hashCode() - Method in class org.molgenis.omx.observ.value.IntValue
hashCode() - Method in class org.molgenis.omx.observ.value.LongValue
hashCode() - Method in class org.molgenis.omx.observ.value.MrefValue
hashCode() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
hashCode() - Method in class org.molgenis.omx.observ.value.StringValue
hashCode() - Method in class org.molgenis.omx.observ.value.TextValue
hashCode() - Method in class org.molgenis.omx.observ.value.Value
hashCode() - Method in class org.molgenis.omx.observ.value.XrefValue
hashCode() - Method in class org.molgenis.omx.RepositoryTemplateLoader.TemplateSource
hashCode() - Method in class org.molgenis.omx.utils.ValueCell
hasValidFileStorage(DataService) - Method in class org.molgenis.omx.services.StorageHandler: Ask if these is a valid file storage location available.
HtmlValue - Class in org.molgenis.omx.observ.value: HtmlValue: .
HtmlValue() - Constructor for class org.molgenis.omx.observ.value.HtmlValue
HtmlValueMetaData - Class in org.molgenis.omx.observ.value
HtmlValueMetaData() - Constructor for class org.molgenis.omx.observ.value.HtmlValueMetaData
HtmlValueRepository - Class in org.molgenis.omx.observ.value
HtmlValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.HtmlValueRepository
HtmlValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.HtmlValueRepository: For testing purposes
HyperlinkValue - Class in org.molgenis.omx.observ.value: HyperlinkValue: .
HyperlinkValue() - Constructor for class org.molgenis.omx.observ.value.HyperlinkValue
HyperlinkValueDecorator - Class in org.molgenis.omx.decorators
HyperlinkValueDecorator(CrudRepository) - Constructor for class org.molgenis.omx.decorators.HyperlinkValueDecorator
HyperlinkValueMetaData - Class in org.molgenis.omx.observ.value
HyperlinkValueMetaData() - Constructor for class org.molgenis.omx.observ.value.HyperlinkValueMetaData
HyperlinkValueRepository - Class in org.molgenis.omx.observ.value
HyperlinkValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.HyperlinkValueRepository
HyperlinkValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.HyperlinkValueRepository: For testing purposes

I

I18nTools - Class in org.molgenis.omx.utils: Reads internationalized strings of the form {"en":"car", "nl":"auto"}
I18nTools() - Constructor for class org.molgenis.omx.utils.I18nTools
ID - Static variable in class org.molgenis.omx.auth.Institute
ID - Static variable in class org.molgenis.omx.auth.Person
ID - Static variable in class org.molgenis.omx.auth.PersonRole
ID - Static variable in class org.molgenis.omx.core.FreemarkerTemplate
ID - Static variable in class org.molgenis.omx.core.MolgenisEntity
ID - Static variable in class org.molgenis.omx.core.RuntimeProperty
ID - Static variable in class org.molgenis.omx.observ.Category
ID - Static variable in class org.molgenis.omx.observ.Characteristic
ID - Static variable in class org.molgenis.omx.observ.DataSet
ID - Static variable in class org.molgenis.omx.observ.ObservableFeature
ID - Static variable in class org.molgenis.omx.observ.ObservationSet
ID - Static variable in class org.molgenis.omx.observ.ObservationTarget
ID - Static variable in class org.molgenis.omx.observ.ObservedValue
ID - Static variable in class org.molgenis.omx.observ.Protocol
ID - Static variable in class org.molgenis.omx.observ.target.Accession
ID - Static variable in class org.molgenis.omx.observ.target.Individual
ID - Static variable in class org.molgenis.omx.observ.target.Ontology
ID - Static variable in class org.molgenis.omx.observ.target.OntologyTerm
ID - Static variable in class org.molgenis.omx.observ.target.Panel
ID - Static variable in class org.molgenis.omx.observ.target.PanelSource
ID - Static variable in class org.molgenis.omx.observ.target.Species
ID - Static variable in class org.molgenis.omx.observ.value.BoolValue
ID - Static variable in class org.molgenis.omx.observ.value.CategoricalValue
ID - Static variable in class org.molgenis.omx.observ.value.DateTimeValue
ID - Static variable in class org.molgenis.omx.observ.value.DateValue
ID - Static variable in class org.molgenis.omx.observ.value.DecimalValue
ID - Static variable in class org.molgenis.omx.observ.value.EmailValue
ID - Static variable in class org.molgenis.omx.observ.value.HtmlValue
ID - Static variable in class org.molgenis.omx.observ.value.HyperlinkValue
ID - Static variable in class org.molgenis.omx.observ.value.IntValue
ID - Static variable in class org.molgenis.omx.observ.value.LongValue
ID - Static variable in class org.molgenis.omx.observ.value.MrefValue
ID - Static variable in class org.molgenis.omx.observ.value.StringValue
ID - Static variable in class org.molgenis.omx.observ.value.TextValue
ID - Static variable in class org.molgenis.omx.observ.value.Value
ID - Static variable in class org.molgenis.omx.observ.value.XrefValue
Identifiable - Interface in org.molgenis.omx.core: Identifiable: This interface assigns an automatic 'id', globally unique identifier 'identifier' field, and possibly not unique 'name' to all entities that implement it.
IDENTIFIER - Static variable in class org.molgenis.omx.core.RuntimeProperty
IDENTIFIER - Static variable in class org.molgenis.omx.observ.Characteristic
IDENTIFIER - Static variable in class org.molgenis.omx.observ.ObservationSet
IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Ontology
index(DataSetsIndexerController.DataSetIndexRequest) - Method in class org.molgenis.omx.controller.DataSetsIndexerController
index() - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer: Index all datasets
index() - Method in interface org.molgenis.omx.search.DataSetsIndexer
indexDataSets() - Method in class org.molgenis.omx.config.DataExplorerConfig: Indexes datasets at 4 am every night
indexDataSets(List<Object>) - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
indexDataSets(List<Object>) - Method in interface org.molgenis.omx.search.DataSetsIndexer
IndexingEventListener - Class in org.molgenis.omx.search: Indexes not yet indexed DataSets at application startup and when a dataset is imported
IndexingEventListener(DataSetsIndexer) - Constructor for class org.molgenis.omx.search.IndexingEventListener
indexProtocols(List<Object>) - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
indexProtocols(List<Object>) - Method in interface org.molgenis.omx.search.DataSetsIndexer
indexProtocolsSynced(List<Object>) - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
indexProtocolsSynced(List<Object>) - Method in interface org.molgenis.omx.search.DataSetsIndexer
Individual - Class in org.molgenis.omx.observ.target: Individual: The Individuals class defines the subjects that are used as observation target.
Individual() - Constructor for class org.molgenis.omx.observ.target.Individual
IndividualMetaData - Class in org.molgenis.omx.observ.target
IndividualMetaData() - Constructor for class org.molgenis.omx.observ.target.IndividualMetaData
IndividualRepository - Class in org.molgenis.omx.observ.target
IndividualRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.IndividualRepository
IndividualRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.IndividualRepository: For testing purposes
INDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.Panel
INDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals
init(Model) - Method in class org.molgenis.omx.controller.DataSetsIndexerController: Show the explorer page
init(Model) - Method in class org.molgenis.omx.datasetdeleter.DataSetDeleterController
Institute - Class in org.molgenis.omx.auth: Institute: A contact is either a person or an organization.
Institute() - Constructor for class org.molgenis.omx.auth.Institute
InstituteMetaData - Class in org.molgenis.omx.auth
InstituteMetaData() - Constructor for class org.molgenis.omx.auth.InstituteMetaData
InstituteRepository - Class in org.molgenis.omx.auth
InstituteRepository(QueryResolver) - Constructor for class org.molgenis.omx.auth.InstituteRepository
InstituteRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.auth.InstituteRepository: For testing purposes
IntValue - Class in org.molgenis.omx.observ.value: IntValue: .
IntValue() - Constructor for class org.molgenis.omx.observ.value.IntValue
IntValueMetaData - Class in org.molgenis.omx.observ.value
IntValueMetaData() - Constructor for class org.molgenis.omx.observ.value.IntValueMetaData
IntValueRepository - Class in org.molgenis.omx.observ.value
IntValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.IntValueRepository
IntValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.IntValueRepository: For testing purposes
isAbstract() - Method in class org.molgenis.omx.dataset.DataSetEntityMetaData
isAbstract() - Method in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
isAbstract() - Method in class org.molgenis.omx.protocol.ProtocolEntityMetaData
isAggregateable() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isAggregateable() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isAuto() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isAuto() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isIdAtrribute() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isIdAtrribute() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isIndexingRunning() - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
isIndexingRunning() - Method in interface org.molgenis.omx.search.DataSetsIndexer: Check if there is an indexing job running
isLabelAttribute() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isLabelAttribute() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isLookupAttribute() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isLookupAttribute() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
ISMISSING - Static variable in class org.molgenis.omx.observ.Category
isNillable() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isNillable() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isReadonly() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isReadonly() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isSameAs(AttributeMetaData) - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isSameAs(AttributeMetaData) - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isUnique() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isUnique() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
isVisible() - Method in class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
isVisible() - Method in class org.molgenis.omx.protocol.ProtocolAttributeMetaData
iterator() - Method in class org.molgenis.omx.dataset.DataSetMatrixRepository
iterator() - Method in class org.molgenis.omx.protocol.CategoryRepository
iterator() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository
iterator() - Method in class org.molgenis.omx.protocol.ProtocolTreeRepository

J

JDBCMetaDatabase - Class in org.molgenis: This class is an in memory representation of the contents of your *_db.xml file Utility of this class is to allow for dynamic querying and/or user interfacing for example within a query tool or a security module.
JDBCMetaDatabase() - Constructor for class org.molgenis.JDBCMetaDatabase

L

LASTNAME - Static variable in class org.molgenis.omx.auth.Person
LongValue - Class in org.molgenis.omx.observ.value: LongValue: .
LongValue() - Constructor for class org.molgenis.omx.observ.value.LongValue
LongValueMetaData - Class in org.molgenis.omx.observ.value
LongValueMetaData() - Constructor for class org.molgenis.omx.observ.value.LongValueMetaData
LongValueRepository - Class in org.molgenis.omx.observ.value
LongValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.LongValueRepository
LongValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.LongValueRepository: For testing purposes

M

MAXRANGE - Static variable in class org.molgenis.omx.observ.ObservableFeature
MIDINITIALS - Static variable in class org.molgenis.omx.auth.Person
MINRANGE - Static variable in class org.molgenis.omx.observ.ObservableFeature
MolgenisDbSettings - Class in org.molgenis.omx
MolgenisDbSettings(DataService) - Constructor for class org.molgenis.omx.MolgenisDbSettings
MolgenisEntity - Class in org.molgenis.omx.core: MolgenisEntity: Referenceable catalog of entity names, menus, forms and plugins.
MolgenisEntity() - Constructor for class org.molgenis.omx.core.MolgenisEntity
MolgenisEntityMetaData - Class in org.molgenis.omx.core
MolgenisEntityMetaData() - Constructor for class org.molgenis.omx.core.MolgenisEntityMetaData
MolgenisEntityRepository - Class in org.molgenis.omx.core
MolgenisEntityRepository(QueryResolver) - Constructor for class org.molgenis.omx.core.MolgenisEntityRepository
MolgenisEntityRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.core.MolgenisEntityRepository: For testing purposes
molgenisSettings() - Method in class org.molgenis.omx.OmxConfig
MOTHER - Static variable in class org.molgenis.omx.observ.target.Individual
MrefValue - Class in org.molgenis.omx.observ.value: MrefValue: .
MrefValue() - Constructor for class org.molgenis.omx.observ.value.MrefValue
MREFVALUE - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value
MrefValue_Value - Class in org.molgenis.omx.observ.value: MrefValue_Value: Link table for many-to-many relationship 'MrefValue.Value'..
MrefValue_Value() - Constructor for class org.molgenis.omx.observ.value.MrefValue_Value
MrefValue_ValueMetaData - Class in org.molgenis.omx.observ.value
MrefValue_ValueMetaData() - Constructor for class org.molgenis.omx.observ.value.MrefValue_ValueMetaData
MrefValue_ValueRepository - Class in org.molgenis.omx.observ.value
MrefValue_ValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.MrefValue_ValueRepository
MrefValue_ValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.MrefValue_ValueRepository: For testing purposes
MrefValueMetaData - Class in org.molgenis.omx.observ.value
MrefValueMetaData() - Constructor for class org.molgenis.omx.observ.value.MrefValueMetaData
MrefValueRepository - Class in org.molgenis.omx.observ.value
MrefValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.MrefValueRepository
MrefValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.MrefValueRepository: For testing purposes

N

NAME - Static variable in class org.molgenis.omx.auth.Institute
NAME - Static variable in class org.molgenis.omx.core.FreemarkerTemplate
NAME - Static variable in class org.molgenis.omx.core.MolgenisEntity
NAME - Static variable in class org.molgenis.omx.core.RuntimeProperty
NAME - Static variable in class org.molgenis.omx.observ.Characteristic
NAME - Static variable in class org.molgenis.omx.observ.target.Ontology
NameConvention - Class in org.molgenis.omx.decorators: This class contains functions to enforce the XGAP naming policy for entities and storing files that belong to certain entities.
NameConvention() - Constructor for class org.molgenis.omx.decorators.NameConvention
NUMBEROFINDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.Panel
NUMBEROFINDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.PanelSource

O

OBSERVABLEFEATURE - Static variable in class org.molgenis.omx.observ.Category
ObservableFeature - Class in org.molgenis.omx.observ: ObservableFeature: ObservableFeature defines anything that can be observed.
ObservableFeature() - Constructor for class org.molgenis.omx.observ.ObservableFeature
OBSERVABLEFEATURE - Static variable in class org.molgenis.omx.observ.ObservableFeature_Definitions
ObservableFeature_Definitions - Class in org.molgenis.omx.observ: ObservableFeature_definitions: Link table for many-to-many relationship 'ObservableFeature.definitions'..
ObservableFeature_Definitions() - Constructor for class org.molgenis.omx.observ.ObservableFeature_Definitions
ObservableFeature_DefinitionsMetaData - Class in org.molgenis.omx.observ
ObservableFeature_DefinitionsMetaData() - Constructor for class org.molgenis.omx.observ.ObservableFeature_DefinitionsMetaData
ObservableFeature_DefinitionsRepository - Class in org.molgenis.omx.observ
ObservableFeature_DefinitionsRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservableFeature_DefinitionsRepository
ObservableFeature_DefinitionsRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservableFeature_DefinitionsRepository: For testing purposes
ObservableFeatureAttributeMetaData - Class in org.molgenis.omx.protocol
ObservableFeatureAttributeMetaData(ObservableFeature) - Constructor for class org.molgenis.omx.protocol.ObservableFeatureAttributeMetaData
ObservableFeatureMetaData - Class in org.molgenis.omx.observ
ObservableFeatureMetaData() - Constructor for class org.molgenis.omx.observ.ObservableFeatureMetaData
ObservableFeatureRepository - Class in org.molgenis.omx.observ
ObservableFeatureRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservableFeatureRepository
ObservableFeatureRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservableFeatureRepository: For testing purposes
ObservationSet - Class in org.molgenis.omx.observ: ObservationSet: In practice: Observation is one row within a DataSet.
ObservationSet() - Constructor for class org.molgenis.omx.observ.ObservationSet
OBSERVATIONSET - Static variable in class org.molgenis.omx.observ.ObservedValue
ObservationSetMetaData - Class in org.molgenis.omx.observ
ObservationSetMetaData() - Constructor for class org.molgenis.omx.observ.ObservationSetMetaData
ObservationSetRepository - Class in org.molgenis.omx.observ
ObservationSetRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservationSetRepository
ObservationSetRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservationSetRepository: For testing purposes
ObservationTarget - Class in org.molgenis.omx.observ: ObservationTarget: ObservationTarget defines subjects of observation, such as Individual, Panel, Sample, etc.
ObservationTarget() - Constructor for class org.molgenis.omx.observ.ObservationTarget
ObservationTargetMetaData - Class in org.molgenis.omx.observ
ObservationTargetMetaData() - Constructor for class org.molgenis.omx.observ.ObservationTargetMetaData
ObservationTargetRepository - Class in org.molgenis.omx.observ
ObservationTargetRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservationTargetRepository
ObservationTargetRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservationTargetRepository: For testing purposes
ObservedValue - Class in org.molgenis.omx.observ: ObservedValue: Generic storage of values as part of one observation event.
ObservedValue() - Constructor for class org.molgenis.omx.observ.ObservedValue
ObservedValueMetaData - Class in org.molgenis.omx.observ
ObservedValueMetaData() - Constructor for class org.molgenis.omx.observ.ObservedValueMetaData
ObservedValueRepository - Class in org.molgenis.omx.observ
ObservedValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservedValueRepository
ObservedValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ObservedValueRepository: For testing purposes
OmxConfig - Class in org.molgenis.omx
OmxConfig() - Constructor for class org.molgenis.omx.OmxConfig
OmxLookupTableEntityMetaData - Class in org.molgenis.omx.protocol
OmxLookupTableEntityMetaData(ObservableFeature) - Constructor for class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
OmxLookupTableRepository - Class in org.molgenis.omx.protocol
OmxLookupTableRepository(DataService, String, QueryResolver) - Constructor for class org.molgenis.omx.protocol.OmxLookupTableRepository
OmxLookupTableRepositoryRegistrator - Class in org.molgenis.omx.protocol: On startup add an OmxLookupTableRepositoryRegistrator to the DataService for each categorical ObservableFeature
OmxLookupTableRepositoryRegistrator(DataService, QueryResolver) - Constructor for class org.molgenis.omx.protocol.OmxLookupTableRepositoryRegistrator
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.omx.protocol.OmxLookupTableRepositoryRegistrator
onApplicationEvent(ApplicationEvent) - Method in class org.molgenis.omx.search.IndexingEventListener
Ontology - Class in org.molgenis.omx.observ.target: Ontology: Ontology defines a reference to an ontology or controlled vocabulary from which well-defined and stable (ontology) terms can be obtained.
Ontology() - Constructor for class org.molgenis.omx.observ.target.Ontology
ONTOLOGY - Static variable in class org.molgenis.omx.observ.target.OntologyTerm
ONTOLOGYACCESSION - Static variable in class org.molgenis.omx.observ.target.Ontology
OntologyMetaData - Class in org.molgenis.omx.observ.target
OntologyMetaData() - Constructor for class org.molgenis.omx.observ.target.OntologyMetaData
OntologyRepository - Class in org.molgenis.omx.observ.target
OntologyRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.OntologyRepository
OntologyRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.OntologyRepository: For testing purposes
OntologyTerm - Class in org.molgenis.omx.observ.target: OntologyTerm: OntologyTerm defines a single entry (term) from an ontology or a controlled vocabulary (defined by Ontology).
OntologyTerm() - Constructor for class org.molgenis.omx.observ.target.OntologyTerm
OntologyTermMetaData - Class in org.molgenis.omx.observ.target
OntologyTermMetaData() - Constructor for class org.molgenis.omx.observ.target.OntologyTermMetaData
OntologyTermRepository - Class in org.molgenis.omx.observ.target
OntologyTermRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.OntologyTermRepository
OntologyTermRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.OntologyTermRepository: For testing purposes
ONTOLOGYURI - Static variable in class org.molgenis.omx.observ.target.Ontology
org.molgenis - package org.molgenis
org.molgenis.omx - package org.molgenis.omx
org.molgenis.omx.auth - package org.molgenis.omx.auth
org.molgenis.omx.config - package org.molgenis.omx.config
org.molgenis.omx.controller - package org.molgenis.omx.controller
org.molgenis.omx.converters - package org.molgenis.omx.converters
org.molgenis.omx.core - package org.molgenis.omx.core
org.molgenis.omx.dataset - package org.molgenis.omx.dataset
org.molgenis.omx.datasetdeleter - package org.molgenis.omx.datasetdeleter
org.molgenis.omx.decorators - package org.molgenis.omx.decorators
org.molgenis.omx.observ - package org.molgenis.omx.observ
org.molgenis.omx.observ.target - package org.molgenis.omx.observ.target
org.molgenis.omx.observ.value - package org.molgenis.omx.observ.value
org.molgenis.omx.protocol - package org.molgenis.omx.protocol
org.molgenis.omx.search - package org.molgenis.omx.search
org.molgenis.omx.services - package org.molgenis.omx.services
org.molgenis.omx.utils - package org.molgenis.omx.utils

P

Panel - Class in org.molgenis.omx.observ.target: Panel: The Panel class defines groups of individuals based on cohort design, case/controls, families, etc.
Panel() - Constructor for class org.molgenis.omx.observ.target.Panel
PANEL - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals
Panel_Individuals - Class in org.molgenis.omx.observ.target: Panel_Individuals: Link table for many-to-many relationship 'Panel.Individuals'..
Panel_Individuals() - Constructor for class org.molgenis.omx.observ.target.Panel_Individuals
Panel_IndividualsMetaData - Class in org.molgenis.omx.observ.target
Panel_IndividualsMetaData() - Constructor for class org.molgenis.omx.observ.target.Panel_IndividualsMetaData
Panel_IndividualsRepository - Class in org.molgenis.omx.observ.target
Panel_IndividualsRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.Panel_IndividualsRepository
Panel_IndividualsRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.Panel_IndividualsRepository: For testing purposes
PanelMetaData - Class in org.molgenis.omx.observ.target
PanelMetaData() - Constructor for class org.molgenis.omx.observ.target.PanelMetaData
PanelRepository - Class in org.molgenis.omx.observ.target
PanelRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.PanelRepository
PanelRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.PanelRepository: For testing purposes
PanelSource - Class in org.molgenis.omx.observ.target: PanelSource: PanelSources is partOf Panel to define how panels are related panels, founder panels, such as overlap, selection criteria, getting assayed panel from a sample panel, etc.
PanelSource() - Constructor for class org.molgenis.omx.observ.target.PanelSource
PanelSourceMetaData - Class in org.molgenis.omx.observ.target
PanelSourceMetaData() - Constructor for class org.molgenis.omx.observ.target.PanelSourceMetaData
PanelSourceRepository - Class in org.molgenis.omx.observ.target
PanelSourceRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.PanelSourceRepository
PanelSourceRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.PanelSourceRepository: For testing purposes
PANELTYPE - Static variable in class org.molgenis.omx.observ.target.Panel
PARTOFDATASET - Static variable in class org.molgenis.omx.observ.ObservationSet
Person - Class in org.molgenis.omx.auth: Person: Person represents one or more people involved with an Investigation.
Person() - Constructor for class org.molgenis.omx.auth.Person
PersonInterface - Interface in org.molgenis.omx.auth: PersonInterface: A contact is either a person or an organization.
PersonMetaData - Class in org.molgenis.omx.auth
PersonMetaData() - Constructor for class org.molgenis.omx.auth.PersonMetaData
PersonRepository - Class in org.molgenis.omx.auth
PersonRepository(QueryResolver) - Constructor for class org.molgenis.omx.auth.PersonRepository
PersonRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.auth.PersonRepository: For testing purposes
PersonRole - Class in org.molgenis.omx.auth: PersonRole: Seperate type of ontologyTerm to administrate roles.
PersonRole() - Constructor for class org.molgenis.omx.auth.PersonRole
PersonRoleMetaData - Class in org.molgenis.omx.auth
PersonRoleMetaData() - Constructor for class org.molgenis.omx.auth.PersonRoleMetaData
PersonRoleRepository - Class in org.molgenis.omx.auth
PersonRoleRepository(QueryResolver) - Constructor for class org.molgenis.omx.auth.PersonRoleRepository
PersonRoleRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.auth.PersonRoleRepository: For testing purposes
PHONE - Static variable in class org.molgenis.omx.auth.Institute
PHONE - Static variable in class org.molgenis.omx.auth.Person
POSTFIX_OMXLOOKUPTABLE_NAME - Static variable in class org.molgenis.omx.protocol.OmxLookupTableEntityMetaData
propertyExists(String) - Method in class org.molgenis.omx.MolgenisDbSettings
Protocol - Class in org.molgenis.omx.observ: Protocol: The Protocol class defines parameterizable descriptions of (analysis)methods.
Protocol() - Constructor for class org.molgenis.omx.observ.Protocol
PROTOCOL - Static variable in class org.molgenis.omx.observ.Protocol_Features
PROTOCOL - Static variable in class org.molgenis.omx.observ.Protocol_RequiredFeatures
PROTOCOL - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols
Protocol_Features - Class in org.molgenis.omx.observ: Protocol_Features: Link table for many-to-many relationship 'Protocol.Features'..
Protocol_Features() - Constructor for class org.molgenis.omx.observ.Protocol_Features
Protocol_FeaturesMetaData - Class in org.molgenis.omx.observ
Protocol_FeaturesMetaData() - Constructor for class org.molgenis.omx.observ.Protocol_FeaturesMetaData
Protocol_FeaturesRepository - Class in org.molgenis.omx.observ
Protocol_FeaturesRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_FeaturesRepository
Protocol_FeaturesRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_FeaturesRepository: For testing purposes
Protocol_RequiredFeatures - Class in org.molgenis.omx.observ: Protocol_RequiredFeatures: Link table for many-to-many relationship 'Protocol.RequiredFeatures'..
Protocol_RequiredFeatures() - Constructor for class org.molgenis.omx.observ.Protocol_RequiredFeatures
Protocol_RequiredFeaturesMetaData - Class in org.molgenis.omx.observ
Protocol_RequiredFeaturesMetaData() - Constructor for class org.molgenis.omx.observ.Protocol_RequiredFeaturesMetaData
Protocol_RequiredFeaturesRepository - Class in org.molgenis.omx.observ
Protocol_RequiredFeaturesRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_RequiredFeaturesRepository
Protocol_RequiredFeaturesRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_RequiredFeaturesRepository: For testing purposes
Protocol_Subprotocols - Class in org.molgenis.omx.observ: Protocol_subprotocols: Link table for many-to-many relationship 'Protocol.subprotocols'..
Protocol_Subprotocols() - Constructor for class org.molgenis.omx.observ.Protocol_Subprotocols
Protocol_SubprotocolsMetaData - Class in org.molgenis.omx.observ
Protocol_SubprotocolsMetaData() - Constructor for class org.molgenis.omx.observ.Protocol_SubprotocolsMetaData
Protocol_SubprotocolsRepository - Class in org.molgenis.omx.observ
Protocol_SubprotocolsRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_SubprotocolsRepository
Protocol_SubprotocolsRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.Protocol_SubprotocolsRepository: For testing purposes
ProtocolAttributeMetaData - Class in org.molgenis.omx.protocol
ProtocolAttributeMetaData(Protocol) - Constructor for class org.molgenis.omx.protocol.ProtocolAttributeMetaData
ProtocolEntityMetaData - Class in org.molgenis.omx.protocol
ProtocolEntityMetaData(Protocol) - Constructor for class org.molgenis.omx.protocol.ProtocolEntityMetaData
ProtocolMetaData - Class in org.molgenis.omx.observ
ProtocolMetaData() - Constructor for class org.molgenis.omx.observ.ProtocolMetaData
ProtocolRepository - Class in org.molgenis.omx.observ
ProtocolRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.ProtocolRepository
ProtocolRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.ProtocolRepository: For testing purposes
ProtocolTreeRepository - Class in org.molgenis.omx.protocol
ProtocolTreeRepository(Protocol, DataService, String) - Constructor for class org.molgenis.omx.protocol.ProtocolTreeRepository
PROTOCOLTYPE - Static variable in class org.molgenis.omx.observ.Protocol
PROTOCOLUSED - Static variable in class org.molgenis.omx.observ.DataSet
ProtocolUtils - Class in org.molgenis.omx.utils
ProtocolUtils() - Constructor for class org.molgenis.omx.utils.ProtocolUtils

Q

query() - Method in class org.molgenis.omx.protocol.OmxLookupTableRepository

R

Report - Class in org.molgenis.omx.services
Report() - Constructor for class org.molgenis.omx.services.Report
RepositoryTemplateLoader - Class in org.molgenis.omx: Loads FreemarkerTemplates from a repository.
RepositoryTemplateLoader(Queryable) - Constructor for class org.molgenis.omx.RepositoryTemplateLoader
RepositoryTemplateLoader.TemplateSource - Class in org.molgenis.omx: Template source class.
RepositoryTemplateLoader.TemplateSource(FreemarkerTemplate) - Constructor for class org.molgenis.omx.RepositoryTemplateLoader.TemplateSource
REQUIREDFEATURES - Static variable in class org.molgenis.omx.observ.Protocol
REQUIREDFEATURES - Static variable in class org.molgenis.omx.observ.Protocol_RequiredFeatures
ROLES - Static variable in class org.molgenis.omx.auth.Person
ROOT - Static variable in class org.molgenis.omx.observ.Protocol
RuntimeProperty - Class in org.molgenis.omx.core: RuntimeProperty: .
RuntimeProperty() - Constructor for class org.molgenis.omx.core.RuntimeProperty
RuntimePropertyMetaData - Class in org.molgenis.omx.core
RuntimePropertyMetaData() - Constructor for class org.molgenis.omx.core.RuntimePropertyMetaData
RuntimePropertyRepository - Class in org.molgenis.omx.core
RuntimePropertyRepository(QueryResolver) - Constructor for class org.molgenis.omx.core.RuntimePropertyRepository
RuntimePropertyRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.core.RuntimePropertyRepository: For testing purposes

S

SELECTIONCRITERIA - Static variable in class org.molgenis.omx.observ.target.PanelSource
set(Entity, boolean) - Method in class org.molgenis.omx.auth.Institute
set(String, Object) - Method in class org.molgenis.omx.auth.Institute
set(Entity, boolean) - Method in class org.molgenis.omx.auth.Person
set(String, Object) - Method in class org.molgenis.omx.auth.Person
set(Entity, boolean) - Method in class org.molgenis.omx.auth.PersonRole
set(String, Object) - Method in class org.molgenis.omx.auth.PersonRole
set(Entity, boolean) - Method in class org.molgenis.omx.core.FreemarkerTemplate
set(String, Object) - Method in class org.molgenis.omx.core.FreemarkerTemplate
set(Entity, boolean) - Method in class org.molgenis.omx.core.MolgenisEntity
set(String, Object) - Method in class org.molgenis.omx.core.MolgenisEntity
set(Entity, boolean) - Method in class org.molgenis.omx.core.RuntimeProperty
set(String, Object) - Method in class org.molgenis.omx.core.RuntimeProperty
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Category
set(String, Object) - Method in class org.molgenis.omx.observ.Category
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Characteristic
set(String, Object) - Method in class org.molgenis.omx.observ.Characteristic
set(Entity, boolean) - Method in class org.molgenis.omx.observ.DataSet
set(String, Object) - Method in class org.molgenis.omx.observ.DataSet
set(Entity, boolean) - Method in class org.molgenis.omx.observ.ObservableFeature
set(String, Object) - Method in class org.molgenis.omx.observ.ObservableFeature
set(Entity, boolean) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
set(String, Object) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
set(Entity, boolean) - Method in class org.molgenis.omx.observ.ObservationSet
set(String, Object) - Method in class org.molgenis.omx.observ.ObservationSet
set(Entity, boolean) - Method in class org.molgenis.omx.observ.ObservationTarget
set(String, Object) - Method in class org.molgenis.omx.observ.ObservationTarget
set(Entity, boolean) - Method in class org.molgenis.omx.observ.ObservedValue
set(String, Object) - Method in class org.molgenis.omx.observ.ObservedValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Protocol
set(String, Object) - Method in class org.molgenis.omx.observ.Protocol
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Protocol_Features
set(String, Object) - Method in class org.molgenis.omx.observ.Protocol_Features
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
set(String, Object) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
set(Entity, boolean) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
set(String, Object) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Accession
set(String, Object) - Method in class org.molgenis.omx.observ.target.Accession
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Individual
set(String, Object) - Method in class org.molgenis.omx.observ.target.Individual
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Ontology
set(String, Object) - Method in class org.molgenis.omx.observ.target.Ontology
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.OntologyTerm
set(String, Object) - Method in class org.molgenis.omx.observ.target.OntologyTerm
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Panel
set(String, Object) - Method in class org.molgenis.omx.observ.target.Panel
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Panel_Individuals
set(String, Object) - Method in class org.molgenis.omx.observ.target.Panel_Individuals
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.PanelSource
set(String, Object) - Method in class org.molgenis.omx.observ.target.PanelSource
set(Entity, boolean) - Method in class org.molgenis.omx.observ.target.Species
set(String, Object) - Method in class org.molgenis.omx.observ.target.Species
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.BoolValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.BoolValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.CategoricalValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.CategoricalValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.DateTimeValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.DateTimeValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.DateValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.DateValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.DecimalValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.DecimalValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.EmailValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.EmailValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.HtmlValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.HtmlValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.HyperlinkValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.HyperlinkValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.IntValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.IntValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.LongValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.LongValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.MrefValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.MrefValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.MrefValue_Value
set(String, Object) - Method in class org.molgenis.omx.observ.value.MrefValue_Value
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.StringValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.StringValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.TextValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.TextValue
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.Value
set(String, Object) - Method in class org.molgenis.omx.observ.value.Value
set(Entity, boolean) - Method in class org.molgenis.omx.observ.value.XrefValue
set(String, Object) - Method in class org.molgenis.omx.observ.value.XrefValue
set__Type(String) - Method in class org.molgenis.omx.observ.Characteristic: Set the Subtypes have to be set to allow searching.
set__Type(String) - Method in class org.molgenis.omx.observ.value.Value: Set the Subtypes have to be set to allow searching.
setActive(Boolean) - Method in class org.molgenis.omx.observ.Protocol: Set the whether this protocol is considered active/inactive.
setAddress(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setAddress(String) - Method in class org.molgenis.omx.auth.Institute: Set the The address of the Contact..
setAddress(String) - Method in class org.molgenis.omx.auth.Person: Set the The address of the Contact..
setAddress(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setAffiliation(Institute) - Method in class org.molgenis.omx.auth.Person: Set the .
setAffiliation(Institute) - Method in interface org.molgenis.omx.auth.PersonInterface
setAutoid(Integer) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.observ.Protocol_Features: Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Set the automatic id field to ensure ordering of mrefs.
setCity(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setCity(String) - Method in class org.molgenis.omx.auth.Institute: Set the Added from the old definition of MolgenisUser.
setCity(String) - Method in class org.molgenis.omx.auth.Person: Set the Added from the old definition of MolgenisUser.
setCity(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setClassName(String) - Method in class org.molgenis.omx.core.MolgenisEntity: Set the Full name of the entity.
setCountry(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setCountry(String) - Method in class org.molgenis.omx.auth.Institute: Set the Added from the old definition of MolgenisUser.
setCountry(String) - Method in class org.molgenis.omx.auth.Person: Set the Added from the old definition of MolgenisUser.
setCountry(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setCurrentPanel(Panel) - Method in class org.molgenis.omx.observ.target.PanelSource: Set the Panel for which these sources are defined..
setDataType(String) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the (Optional) Reference to the technical data type.
setDefinition(OntologyTerm) - Method in class org.molgenis.omx.observ.Category: Set the The category that is being measured in a specific way..
setDefinition(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm: Set the (Optional) The definition of the term..
setDefinitions(List<OntologyTerm>) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the The concept that is being measured in a specific way..
setDefinitions(OntologyTerm) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Set the .
setDefinitionsObservableFeatureCollection(Collection<ObservableFeature>) - Method in class org.molgenis.omx.observ.target.OntologyTerm
setDepartment(String) - Method in class org.molgenis.omx.auth.Person: Set the Added from the old definition of MolgenisUser.
setDepartment(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setDescription(String) - Method in class org.molgenis.omx.observ.Characteristic: Set the (Optional) Rudimentary meta data about the observable feature.
setEmail(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setEmail(String) - Method in class org.molgenis.omx.auth.Institute: Set the The email address of the Contact..
setEmail(String) - Method in class org.molgenis.omx.auth.Person: Set the The email address of the Contact..
setEmail(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setEndTime(Date) - Method in class org.molgenis.omx.observ.DataSet: Set the (Optional) time when the protocol ended..
setFather(Individual) - Method in class org.molgenis.omx.observ.target.Individual: Set the Refers to the father of the individual..
setFax(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setFax(String) - Method in class org.molgenis.omx.auth.Institute: Set the The fax number of the Contact..
setFax(String) - Method in class org.molgenis.omx.auth.Person: Set the The fax number of the Contact..
setFax(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setFeature(ObservableFeature) - Method in class org.molgenis.omx.observ.ObservedValue: Set the References the ObservableFeature that this observation was made on.
setFeatures(List<ObservableFeature>) - Method in class org.molgenis.omx.observ.Protocol: Set the parameters (in/out) that are used or produced by this protocol..
setFeatures(ObservableFeature) - Method in class org.molgenis.omx.observ.Protocol_Features: Set the .
setFeaturesProtocolCollection(Collection<Protocol>) - Method in class org.molgenis.omx.observ.ObservableFeature
setFileStorage(File) - Method in class org.molgenis.omx.services.Report
setFileStorage(String, DataService) - Method in class org.molgenis.omx.services.StorageHandler: Save this path in the form of a string to the file storage path entity.
setFileStoragePropsPresent(Boolean) - Method in class org.molgenis.omx.services.Report
setFirstName(String) - Method in class org.molgenis.omx.auth.Person: Set the .
setFirstName(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setFolderExists(Boolean) - Method in class org.molgenis.omx.services.Report
setFolderHasContent(Boolean) - Method in class org.molgenis.omx.services.Report
setId(Integer) - Method in interface org.molgenis.omx.core.Autoid
setId(Integer) - Method in class org.molgenis.omx.core.FreemarkerTemplate: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.core.MolgenisEntity: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.core.RuntimeProperty: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.Characteristic: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.ObservationSet: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.ObservedValue: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.target.Ontology: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource: Set the automatically generated internal id, only for internal use..
setId(Integer) - Method in class org.molgenis.omx.observ.value.Value: Set the automatically generated internal id, only for internal use..
setIdentifier(String) - Method in interface org.molgenis.omx.core.Identifiable
setIdentifier(String) - Method in class org.molgenis.omx.core.RuntimeProperty: Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
setIdentifier(String) - Method in class org.molgenis.omx.observ.Characteristic: Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
setIdentifier(String) - Method in class org.molgenis.omx.observ.ObservationSet: Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
setIdentifier(String) - Method in class org.molgenis.omx.observ.target.Ontology: Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
setIndividuals(List<Individual>) - Method in class org.molgenis.omx.observ.target.Panel: Set the The list of individuals in this panel.
setIndividuals(Individual) - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Set the .
setIndividualsPanelCollection(Collection<Panel>) - Method in class org.molgenis.omx.observ.target.Individual
setIsMissing(Boolean) - Method in class org.molgenis.omx.observ.Category: Set the whether this value should be treated as missing value..
setLastName(String) - Method in class org.molgenis.omx.auth.Person: Set the .
setLastName(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setMaxRange(Long) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the for numeric values this is used to set the 'max' value of the slider user interface.
setMidInitials(String) - Method in class org.molgenis.omx.auth.Person: Set the .
setMidInitials(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setMinRange(Long) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the for numeric values this is used to set the 'min' value of the slider user interface.
setMother(Individual) - Method in class org.molgenis.omx.observ.target.Individual: Set the Refers to the mother of the individual..
setMrefValue(MrefValue) - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Set the .
setName(String) - Method in class org.molgenis.omx.auth.Institute: Set the .
setName(String) - Method in class org.molgenis.omx.core.FreemarkerTemplate: Set the Name of the entity.
setName(String) - Method in interface org.molgenis.omx.core.Identifiable
setName(String) - Method in class org.molgenis.omx.core.MolgenisEntity: Set the Name of the entity.
setName(String) - Method in class org.molgenis.omx.core.RuntimeProperty: Set the human readible name, not necessary unique..
setName(String) - Method in class org.molgenis.omx.observ.Characteristic: Set the human readible name, not necessary unique..
setName(String) - Method in class org.molgenis.omx.observ.target.Ontology: Set the human readible name, not necessary unique..
setNumberOfIndividuals(Integer) - Method in class org.molgenis.omx.observ.target.Panel: Set the .
setNumberOfIndividuals(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource: Set the Number of individuals lifted over from this source.
setObservableFeature(ObservableFeature) - Method in class org.molgenis.omx.observ.Category: Set the The Measurement these permitted values are part of..
setObservableFeature(ObservableFeature) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions: Set the .
setObservationSet(ObservationSet) - Method in class org.molgenis.omx.observ.ObservedValue: Set the Reference to the observation.
setOntology(Ontology) - Method in class org.molgenis.omx.observ.target.OntologyTerm: Set the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
setOntologyAccession(String) - Method in class org.molgenis.omx.observ.target.Ontology: Set the A accession that uniquely identifies the ontology (typically an acronym).
setOntologyURI(String) - Method in class org.molgenis.omx.observ.target.Ontology: Set the (Optional) A URI that references the location of the ontology..
setPanel(Panel) - Method in class org.molgenis.omx.observ.target.Panel_Individuals: Set the .
setPanelType(OntologyTerm) - Method in class org.molgenis.omx.observ.target.Panel: 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).
setPartOfDataSet(DataSet) - Method in class org.molgenis.omx.observ.ObservationSet: Set the DataSet this ValueSet is part of..
setPhone(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setPhone(String) - Method in class org.molgenis.omx.auth.Institute: Set the The telephone number of the Contact including the suitable area codes..
setPhone(String) - Method in class org.molgenis.omx.auth.Person: Set the The telephone number of the Contact including the suitable area codes..
setPhone(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setProperty(String, String) - Method in class org.molgenis.omx.MolgenisDbSettings
setProtocol(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Features: Set the .
setProtocol(Protocol) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Set the .
setProtocol(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Set the .
setProtocolType(OntologyTerm) - Method in class org.molgenis.omx.observ.Protocol: Set the classification of protocol.
setProtocolUsed(Protocol) - Method in class org.molgenis.omx.observ.DataSet: Set the Reference to the protocol that is being used (if available).
setRequiredFeatures(List<ObservableFeature>) - Method in class org.molgenis.omx.observ.Protocol: Set the ...........
setRequiredFeatures(ObservableFeature) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures: Set the .
setRequiredFeaturesProtocolCollection(Collection<Protocol>) - Method in class org.molgenis.omx.observ.ObservableFeature
setRoles(PersonRole) - Method in class org.molgenis.omx.auth.Person: Set the Indicate role of the contact, e.g.
setRoles(PersonRole) - Method in interface org.molgenis.omx.auth.PersonInterface
setRoot(Boolean) - Method in class org.molgenis.omx.observ.Protocol: Set the Indicator whether this protocol defines a workflow (e.g is the first protocol of a workflow)..
setSearchService(SearchService) - Method in class org.molgenis.omx.search.AsyncDataSetsIndexer
setSelectionCriteria(String) - Method in class org.molgenis.omx.observ.target.PanelSource: Set the Inclusion/exclusion criteria used to select these individuals from source into current panel.
setSourcePanel(Panel) - Method in class org.molgenis.omx.observ.target.PanelSource: Set the Source that contributed individuals to current panel.
setSpecies(Species) - Method in class org.molgenis.omx.observ.target.Panel: Set the The species this panel is an instance of/part of/extracted from..
setStartTime(Date) - Method in class org.molgenis.omx.observ.DataSet: Set the time when the protocol started..
setSubprotocols(List<Protocol>) - Method in class org.molgenis.omx.observ.Protocol: Set the Subprotocols of this protocol.
setSubprotocols(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols: Set the .
setSubprotocolsProtocolCollection(Collection<Protocol>) - Method in class org.molgenis.omx.observ.Protocol
setTemporal(Boolean) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the Whether this feature is time dependent and can have different values when measured on different times (e.g.
setTermAccession(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm: Set the (Optional) The accession number assigned to the ontology term in its source ontology.
setTime(Date) - Method in class org.molgenis.omx.observ.ObservationSet: Set the Time of this observationSet.
setTitle(String) - Method in class org.molgenis.omx.auth.Person: Set the An academic title, e.g.
setTitle(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setTollFreePhone(String) - Method in interface org.molgenis.omx.auth.ContactInterface
setTollFreePhone(String) - Method in class org.molgenis.omx.auth.Institute: Set the A toll free phone number for the Contact, including suitable area codes..
setTollFreePhone(String) - Method in class org.molgenis.omx.auth.Person: Set the A toll free phone number for the Contact, including suitable area codes..
setTollFreePhone(String) - Method in interface org.molgenis.omx.auth.PersonInterface
setType(String) - Method in class org.molgenis.omx.core.MolgenisEntity: Set the Type of the entity.
setUnit(OntologyTerm) - Method in class org.molgenis.omx.observ.ObservableFeature: Set the (Optional) Reference to the well-defined measurement unit used to observe this feature (if feature is that concrete).
setValue(String) - Method in class org.molgenis.omx.core.FreemarkerTemplate: Set the .
setValue(String) - Method in class org.molgenis.omx.core.RuntimeProperty: Set the .
setValue(Value) - Method in class org.molgenis.omx.observ.ObservedValue: Set the The value observed.
setValue(Boolean) - Method in class org.molgenis.omx.observ.value.BoolValue: Set the .
setValue(Category) - Method in class org.molgenis.omx.observ.value.CategoricalValue: Set the .
setValue(Date) - Method in class org.molgenis.omx.observ.value.DateTimeValue: Set the .
setValue(Date) - Method in class org.molgenis.omx.observ.value.DateValue: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.DateValue: Set the .
setValue(Double) - Method in class org.molgenis.omx.observ.value.DecimalValue: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.EmailValue: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.HtmlValue: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue: Set the .
setValue(Integer) - Method in class org.molgenis.omx.observ.value.IntValue: Set the .
setValue(Long) - Method in class org.molgenis.omx.observ.value.LongValue: Set the .
setValue(List<Characteristic>) - Method in class org.molgenis.omx.observ.value.MrefValue: Set the .
setValue(Characteristic) - Method in class org.molgenis.omx.observ.value.MrefValue_Value: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.StringValue: Set the .
setValue(String) - Method in class org.molgenis.omx.observ.value.TextValue: Set the .
setValue(Characteristic) - Method in class org.molgenis.omx.observ.value.XrefValue: Set the .
setValueCode(String) - Method in class org.molgenis.omx.observ.Category: Set the The value used to store this category in ObservedValue.
setValueMrefValueCollection(Collection<MrefValue>) - Method in class org.molgenis.omx.observ.Characteristic
setVerified(Boolean) - Method in class org.molgenis.omx.services.Report
SOURCEPANEL - Static variable in class org.molgenis.omx.observ.target.PanelSource
SPECIES - Static variable in class org.molgenis.omx.observ.target.Panel
Species - Class in org.molgenis.omx.observ.target: Species: Ontology terms for species.
Species() - Constructor for class org.molgenis.omx.observ.target.Species
SpeciesMetaData - Class in org.molgenis.omx.observ.target
SpeciesMetaData() - Constructor for class org.molgenis.omx.observ.target.SpeciesMetaData
SpeciesRepository - Class in org.molgenis.omx.observ.target
SpeciesRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.target.SpeciesRepository
SpeciesRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.target.SpeciesRepository: For testing purposes
STARTTIME - Static variable in class org.molgenis.omx.observ.DataSet
startUpIndexer() - Method in class org.molgenis.omx.config.DataExplorerConfig: Indexes not yet indexed DataSets at application startup, does not reindex already indexed DataSets (even not when there are chenges)
statusMessage() - Method in class org.molgenis.omx.controller.DataSetsIndexerStatusController
STOPWORDSLIST - Static variable in class org.molgenis.omx.protocol.CategoryRepository
STOPWORDSLIST - Static variable in class org.molgenis.omx.protocol.ProtocolTreeRepository
StorageHandler - Class in org.molgenis.omx.services
StorageHandler(DataService) - Constructor for class org.molgenis.omx.services.StorageHandler: On instantiation, build a simple report of the current state, without running actual validation yet.
StringValue - Class in org.molgenis.omx.observ.value: StringValue: .
StringValue() - Constructor for class org.molgenis.omx.observ.value.StringValue
StringValueMetaData - Class in org.molgenis.omx.observ.value
StringValueMetaData() - Constructor for class org.molgenis.omx.observ.value.StringValueMetaData
StringValueRepository - Class in org.molgenis.omx.observ.value
StringValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.StringValueRepository
StringValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.StringValueRepository: For testing purposes
SUBPROTOCOLS - Static variable in class org.molgenis.omx.observ.Protocol
SUBPROTOCOLS - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols

T

TEMPORAL - Static variable in class org.molgenis.omx.observ.ObservableFeature
TERMACCESSION - Static variable in class org.molgenis.omx.observ.target.OntologyTerm
TextValue - Class in org.molgenis.omx.observ.value: TextValue: .
TextValue() - Constructor for class org.molgenis.omx.observ.value.TextValue
TextValueMetaData - Class in org.molgenis.omx.observ.value
TextValueMetaData() - Constructor for class org.molgenis.omx.observ.value.TextValueMetaData
TextValueRepository - Class in org.molgenis.omx.observ.value
TextValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.TextValueRepository
TextValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.TextValueRepository: For testing purposes
TIME - Static variable in class org.molgenis.omx.observ.ObservationSet
TITLE - Static variable in class org.molgenis.omx.auth.Person
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToBoolValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToCategoricalValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDateTimeValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDateValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToDecimalValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToEmailValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToHtmlValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToHyperlinkValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToIntValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToLongValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToMrefValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToStringValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToTextValueConverter
toCell(Value, ObservableFeature) - Method in interface org.molgenis.omx.converters.EntityToValueConverter: Returns the java type value contained by a value entity
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.EntityToXrefValueConverter
toCell(Value, ObservableFeature) - Method in class org.molgenis.omx.converters.ValueConverter
TOLLFREEPHONE - Static variable in class org.molgenis.omx.auth.Institute
TOLLFREEPHONE - Static variable in class org.molgenis.omx.auth.Person
toString() - Method in class org.molgenis.omx.auth.Institute
toString(boolean) - Method in class org.molgenis.omx.auth.Institute
toString() - Method in class org.molgenis.omx.auth.Person
toString(boolean) - Method in class org.molgenis.omx.auth.Person
toString() - Method in class org.molgenis.omx.auth.PersonRole
toString(boolean) - Method in class org.molgenis.omx.auth.PersonRole
toString() - Method in class org.molgenis.omx.core.FreemarkerTemplate
toString(boolean) - Method in class org.molgenis.omx.core.FreemarkerTemplate
toString() - Method in class org.molgenis.omx.core.MolgenisEntity
toString(boolean) - Method in class org.molgenis.omx.core.MolgenisEntity
toString() - Method in class org.molgenis.omx.core.RuntimeProperty
toString(boolean) - Method in class org.molgenis.omx.core.RuntimeProperty
toString() - Method in class org.molgenis.omx.observ.Category
toString(boolean) - Method in class org.molgenis.omx.observ.Category
toString() - Method in class org.molgenis.omx.observ.Characteristic
toString(boolean) - Method in class org.molgenis.omx.observ.Characteristic
toString() - Method in class org.molgenis.omx.observ.DataSet
toString(boolean) - Method in class org.molgenis.omx.observ.DataSet
toString() - Method in class org.molgenis.omx.observ.ObservableFeature
toString(boolean) - Method in class org.molgenis.omx.observ.ObservableFeature
toString() - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
toString(boolean) - Method in class org.molgenis.omx.observ.ObservableFeature_Definitions
toString() - Method in class org.molgenis.omx.observ.ObservationSet
toString(boolean) - Method in class org.molgenis.omx.observ.ObservationSet
toString() - Method in class org.molgenis.omx.observ.ObservationTarget
toString(boolean) - Method in class org.molgenis.omx.observ.ObservationTarget
toString() - Method in class org.molgenis.omx.observ.ObservedValue
toString(boolean) - Method in class org.molgenis.omx.observ.ObservedValue
toString() - Method in class org.molgenis.omx.observ.Protocol
toString(boolean) - Method in class org.molgenis.omx.observ.Protocol
toString() - Method in class org.molgenis.omx.observ.Protocol_Features
toString(boolean) - Method in class org.molgenis.omx.observ.Protocol_Features
toString() - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
toString(boolean) - Method in class org.molgenis.omx.observ.Protocol_RequiredFeatures
toString() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
toString(boolean) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols
toString() - Method in class org.molgenis.omx.observ.target.Accession
toString(boolean) - Method in class org.molgenis.omx.observ.target.Accession
toString() - Method in class org.molgenis.omx.observ.target.Individual
toString(boolean) - Method in class org.molgenis.omx.observ.target.Individual
toString() - Method in class org.molgenis.omx.observ.target.Ontology
toString(boolean) - Method in class org.molgenis.omx.observ.target.Ontology
toString() - Method in class org.molgenis.omx.observ.target.OntologyTerm
toString(boolean) - Method in class org.molgenis.omx.observ.target.OntologyTerm
toString() - Method in class org.molgenis.omx.observ.target.Panel
toString(boolean) - Method in class org.molgenis.omx.observ.target.Panel
toString() - Method in class org.molgenis.omx.observ.target.Panel_Individuals
toString(boolean) - Method in class org.molgenis.omx.observ.target.Panel_Individuals
toString() - Method in class org.molgenis.omx.observ.target.PanelSource
toString(boolean) - Method in class org.molgenis.omx.observ.target.PanelSource
toString() - Method in class org.molgenis.omx.observ.target.Species
toString(boolean) - Method in class org.molgenis.omx.observ.target.Species
toString() - Method in class org.molgenis.omx.observ.value.BoolValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.BoolValue
toString() - Method in class org.molgenis.omx.observ.value.CategoricalValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.CategoricalValue
toString() - Method in class org.molgenis.omx.observ.value.DateTimeValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.DateTimeValue
toString() - Method in class org.molgenis.omx.observ.value.DateValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.DateValue
toString() - Method in class org.molgenis.omx.observ.value.DecimalValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.DecimalValue
toString() - Method in class org.molgenis.omx.observ.value.EmailValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.EmailValue
toString() - Method in class org.molgenis.omx.observ.value.HtmlValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.HtmlValue
toString() - Method in class org.molgenis.omx.observ.value.HyperlinkValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.HyperlinkValue
toString() - Method in class org.molgenis.omx.observ.value.IntValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.IntValue
toString() - Method in class org.molgenis.omx.observ.value.LongValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.LongValue
toString() - Method in class org.molgenis.omx.observ.value.MrefValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.MrefValue
toString() - Method in class org.molgenis.omx.observ.value.MrefValue_Value
toString(boolean) - Method in class org.molgenis.omx.observ.value.MrefValue_Value
toString() - Method in class org.molgenis.omx.observ.value.StringValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.StringValue
toString() - Method in class org.molgenis.omx.observ.value.TextValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.TextValue
toString() - Method in class org.molgenis.omx.observ.value.Value
toString(boolean) - Method in class org.molgenis.omx.observ.value.Value
toString() - Method in class org.molgenis.omx.observ.value.XrefValue
toString(boolean) - Method in class org.molgenis.omx.observ.value.XrefValue
toString() - Method in class org.molgenis.omx.RepositoryTemplateLoader.TemplateSource
toString() - Method in class org.molgenis.omx.utils.ValueCell
TYPE_ - Static variable in class org.molgenis.omx.core.MolgenisEntity

U

UNIT - Static variable in class org.molgenis.omx.observ.ObservableFeature
update(Entity) - Method in class org.molgenis.omx.decorators.EmailValueDecorator
update(Iterable<? extends Entity>) - Method in class org.molgenis.omx.decorators.EmailValueDecorator
update(Entity) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator
update(Iterable<? extends Entity>) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToBoolValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToCategoricalValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToDateTimeValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToDateValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToDecimalValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToEmailValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToHtmlValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToHyperlinkValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToIntValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToLongValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToMrefValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToStringValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToTextValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in interface org.molgenis.omx.converters.EntityToValueConverter: Updates an existing value by converting an entity column
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.EntityToXrefValueConverter
updateFromEntity(Entity, String, ObservableFeature, Value) - Method in class org.molgenis.omx.converters.ValueConverter
updateProperty(String, String) - Method in class org.molgenis.omx.MolgenisDbSettings
URI - Static variable in class org.molgenis.omx.controller.DataSetsIndexerController
URI - Static variable in class org.molgenis.omx.controller.DataSetsIndexerStatusController
URI - Static variable in class org.molgenis.omx.datasetdeleter.DataSetDeleterController

V

validateEntityName(String) - Static method in class org.molgenis.omx.decorators.NameConvention: Validates an entity name, checking that only characters from the set [<>/a-zA-Z0-9_\\s\\-:.(),;\\+] are used.
validateEntityNames(List<E>) - Static method in class org.molgenis.omx.decorators.NameConvention: Validate names of Entities by wrapping NameConvention.validateEntityName(name)
validateEntityNamesStrict(List<E>) - Static method in class org.molgenis.omx.decorators.NameConvention: Validate names of Entities by wrapping NameConvention.validateEntityNameStrict(name)
validateEntityNameStrict(String) - Static method in class org.molgenis.omx.decorators.NameConvention: Validates an entity name, so that they can be used in contexts such as programming environments where strict names are needed.
validateFileName(String) - Static method in class org.molgenis.omx.decorators.NameConvention: Validates a file name, so that they can be safely stored on any file system.
validateFileStorage(DataService) - Method in class org.molgenis.omx.services.StorageHandler: Run validation check on the current set file storage path.
VALUE - Static variable in class org.molgenis.omx.core.FreemarkerTemplate
VALUE - Static variable in class org.molgenis.omx.core.RuntimeProperty
VALUE - Static variable in class org.molgenis.omx.observ.ObservedValue
VALUE - Static variable in class org.molgenis.omx.observ.value.BoolValue
VALUE - Static variable in class org.molgenis.omx.observ.value.CategoricalValue
VALUE - Static variable in class org.molgenis.omx.observ.value.DateTimeValue
VALUE - Static variable in class org.molgenis.omx.observ.value.DateValue
VALUE - Static variable in class org.molgenis.omx.observ.value.DecimalValue
VALUE - Static variable in class org.molgenis.omx.observ.value.EmailValue
VALUE - Static variable in class org.molgenis.omx.observ.value.HtmlValue
VALUE - Static variable in class org.molgenis.omx.observ.value.HyperlinkValue
VALUE - Static variable in class org.molgenis.omx.observ.value.IntValue
VALUE - Static variable in class org.molgenis.omx.observ.value.LongValue
VALUE - Static variable in class org.molgenis.omx.observ.value.MrefValue
VALUE - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value
VALUE - Static variable in class org.molgenis.omx.observ.value.StringValue
VALUE - Static variable in class org.molgenis.omx.observ.value.TextValue
Value - Class in org.molgenis.omx.observ.value: Value: .
Value() - Constructor for class org.molgenis.omx.observ.value.Value
VALUE - Static variable in class org.molgenis.omx.observ.value.XrefValue
ValueCell<T> - Class in org.molgenis.omx.utils
ValueCell(T) - Constructor for class org.molgenis.omx.utils.ValueCell
ValueCell(String, T) - Constructor for class org.molgenis.omx.utils.ValueCell
ValueCell(Integer, String, T) - Constructor for class org.molgenis.omx.utils.ValueCell
VALUECODE - Static variable in class org.molgenis.omx.observ.Category
ValueConverter - Class in org.molgenis.omx.converters: Converts tuple column values to value entities
ValueConverter(DataService) - Constructor for class org.molgenis.omx.converters.ValueConverter
ValueConverterException - Exception in org.molgenis.omx.converters
ValueConverterException(String) - Constructor for exception org.molgenis.omx.converters.ValueConverterException
ValueConverterException(Exception) - Constructor for exception org.molgenis.omx.converters.ValueConverterException
ValueConverterException(String, Exception) - Constructor for exception org.molgenis.omx.converters.ValueConverterException
ValueMetaData - Class in org.molgenis.omx.observ.value
ValueMetaData() - Constructor for class org.molgenis.omx.observ.value.ValueMetaData
ValueRepository - Class in org.molgenis.omx.observ.value
ValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.ValueRepository
ValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.ValueRepository: For testing purposes

X

XrefValue - Class in org.molgenis.omx.observ.value: XrefValue: .
XrefValue() - Constructor for class org.molgenis.omx.observ.value.XrefValue
XrefValueMetaData - Class in org.molgenis.omx.observ.value
XrefValueMetaData() - Constructor for class org.molgenis.omx.observ.value.XrefValueMetaData
XrefValueRepository - Class in org.molgenis.omx.observ.value
XrefValueRepository(QueryResolver) - Constructor for class org.molgenis.omx.observ.value.XrefValueRepository
XrefValueRepository(EntityManager, QueryResolver) - Constructor for class org.molgenis.omx.observ.value.XrefValueRepository: For testing purposes

_

__TYPE - Static variable in class org.molgenis.omx.observ.Characteristic
__TYPE - Static variable in class org.molgenis.omx.observ.value.Value

A B C D E F G H I J L M N O P Q R S T U V X _