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

A

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

Accession(Accession) - Constructor for class org.molgenis.omx.observ.target.Accession

copy constructor

AccessionEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Accession from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

AccessionEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.AccessionEntityImporter

AccessionForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Accession

AccessionForm() - Constructor for class org.molgenis.omx.observ.target.ui.AccessionForm

AccessionForm(Accession) - Constructor for class org.molgenis.omx.observ.target.ui.AccessionForm

AccessionJpaMapper - Class in org.molgenis.omx.observ.target.db

AccessionJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.AccessionJpaMapper

AccessionService - Class in org.molgenis.service

AccessionService() - Constructor for class org.molgenis.service.AccessionService

add(TupleTable) - Method in class org.molgenis.omx.dataset.DataSetTable

add(List<E>) - Method in class org.molgenis.omx.decorators.EmailValueDecorator

add(List<E>) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator

add(List<E>) - Method in class org.molgenis.omx.decorators.MolgenisFileDecorator

addToCart(ShoppingCartController.FeaturesRequest) - Method in class org.molgenis.omx.cart.ShoppingCartController

Autoid - Interface in org.molgenis.omx.core

Autoid: This interface assigns an automatic 'id'.

AUTOID - Static variable in class org.molgenis.omx.observ.Protocol_Features

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

BoolValue - Class in org.molgenis.omx.observ.value

BoolValue: .

BoolValue() - Constructor for class org.molgenis.omx.observ.value.BoolValue

BoolValue(BoolValue) - Constructor for class org.molgenis.omx.observ.value.BoolValue

copy constructor

BoolValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads BoolValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

BoolValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.BoolValueEntityImporter

BoolValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity BoolValue

BoolValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.BoolValueForm

BoolValueForm(BoolValue) - Constructor for class org.molgenis.omx.observ.value.ui.BoolValueForm

BoolValueJpaMapper - Class in org.molgenis.omx.observ.value.db

BoolValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

BoolValueService - Class in org.molgenis.service

BoolValueService() - Constructor for class org.molgenis.service.BoolValueService

C

CategoricalValue - Class in org.molgenis.omx.observ.value

CategoricalValue: .

CategoricalValue() - Constructor for class org.molgenis.omx.observ.value.CategoricalValue

CategoricalValue(CategoricalValue) - Constructor for class org.molgenis.omx.observ.value.CategoricalValue

copy constructor

CategoricalValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads CategoricalValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

CategoricalValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.CategoricalValueEntityImporter

CategoricalValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity CategoricalValue

CategoricalValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.CategoricalValueForm

CategoricalValueForm(CategoricalValue) - Constructor for class org.molgenis.omx.observ.value.ui.CategoricalValueForm

CategoricalValueJpaMapper - Class in org.molgenis.omx.observ.value.db

CategoricalValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

CategoricalValueService - Class in org.molgenis.service

CategoricalValueService() - Constructor for class org.molgenis.service.CategoricalValueService

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

Category(Category) - Constructor for class org.molgenis.omx.observ.Category

copy constructor

CategoryEntityImporter - Class in org.molgenis.omx.observ.db

Reads Category from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

CategoryEntityImporter() - Constructor for class org.molgenis.omx.observ.db.CategoryEntityImporter

CategoryForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity Category

CategoryForm() - Constructor for class org.molgenis.omx.observ.ui.CategoryForm

CategoryForm(Category) - Constructor for class org.molgenis.omx.observ.ui.CategoryForm

CategoryJpaMapper - Class in org.molgenis.omx.observ.db

CategoryJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.CategoryJpaMapper

CategoryService - Class in org.molgenis.service

CategoryService() - Constructor for class org.molgenis.service.CategoryService

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

Characteristic(Characteristic) - Constructor for class org.molgenis.omx.observ.Characteristic

copy constructor

CharacteristicEntityImporter - Class in org.molgenis.omx.observ.db

Reads Characteristic from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

CharacteristicEntityImporter() - Constructor for class org.molgenis.omx.observ.db.CharacteristicEntityImporter

CharacteristicForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity Characteristic

CharacteristicForm() - Constructor for class org.molgenis.omx.observ.ui.CharacteristicForm

CharacteristicForm(Characteristic) - Constructor for class org.molgenis.omx.observ.ui.CharacteristicForm

CharacteristicJpaMapper - Class in org.molgenis.omx.observ.db

CharacteristicJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.CharacteristicJpaMapper

CharacteristicService - Class in org.molgenis.service

CharacteristicService() - Constructor for class org.molgenis.service.CharacteristicService

CLASSNAME - Static variable in class org.molgenis.omx.core.MolgenisEntity

copyHelper(File, File, boolean) - Static method in class org.molgenis.omx.services.FileUploadUtils

create(MolgenisEntity) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

create(MolgenisFile) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

create(RuntimeProperty) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

create(Tuple) - Method in class org.molgenis.omx.core.MolgenisEntity

create(Tuple) - Method in class org.molgenis.omx.core.MolgenisFile

create(Tuple) - Method in class org.molgenis.omx.core.RuntimeProperty

create(Tuple) - Method in class org.molgenis.omx.observ.Category

create(Tuple) - Method in class org.molgenis.omx.observ.Characteristic

create(Tuple) - Method in class org.molgenis.omx.observ.DataSet

create(Category) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

create(Characteristic) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

create(DataSet) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

create(ObservableFeature) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

create(ObservationSet) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

create(ObservationTarget) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

create(ObservedValue) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

create(Protocol_Features) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

create(Protocol_Subprotocols) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

create(Protocol) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

create(Tuple) - Method in class org.molgenis.omx.observ.ObservableFeature

create(Tuple) - Method in class org.molgenis.omx.observ.ObservationSet

create(Tuple) - Method in class org.molgenis.omx.observ.ObservationTarget

create(Tuple) - Method in class org.molgenis.omx.observ.ObservedValue

create(Tuple) - Method in class org.molgenis.omx.observ.Protocol

create(Tuple) - Method in class org.molgenis.omx.observ.Protocol_Features

create(Tuple) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

create(Tuple) - Method in class org.molgenis.omx.observ.target.Accession

create(Accession) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

create(Individual) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

create(Ontology) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

create(OntologyTerm) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

create(Panel_Individuals) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

create(Panel) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

create(PanelSource) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

create(Species) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

create(Tuple) - Method in class org.molgenis.omx.observ.target.Individual

create(Tuple) - Method in class org.molgenis.omx.observ.target.Ontology

create(Tuple) - Method in class org.molgenis.omx.observ.target.OntologyTerm

create(Tuple) - Method in class org.molgenis.omx.observ.target.Panel

create(Tuple) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

create(Tuple) - Method in class org.molgenis.omx.observ.target.PanelSource

create(Tuple) - Method in class org.molgenis.omx.observ.target.Species

create(Tuple) - Method in class org.molgenis.omx.observ.value.BoolValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.CategoricalValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.DateTimeValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.DateValue

create(BoolValue) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

create(CategoricalValue) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

create(DateTimeValue) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

create(DateValue) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

create(DecimalValue) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

create(EmailValue) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

create(HtmlValue) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

create(HyperlinkValue) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

create(IntValue) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

create(LongValue) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

create(MrefValue_Value) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

create(MrefValue) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

create(StringValue) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

create(TextValue) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

create(Value) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

create(XrefValue) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

create(Tuple) - Method in class org.molgenis.omx.observ.value.DecimalValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.EmailValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.HtmlValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.IntValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.LongValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.MrefValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

create(Tuple) - Method in class org.molgenis.omx.observ.value.StringValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.TextValue

create(Tuple) - Method in class org.molgenis.omx.observ.value.Value

create(Tuple) - Method in class org.molgenis.omx.observ.value.XrefValue

create(Accession) - Method in class org.molgenis.service.AccessionService

create(BoolValue) - Method in class org.molgenis.service.BoolValueService

create(CategoricalValue) - Method in class org.molgenis.service.CategoricalValueService

create(Category) - Method in class org.molgenis.service.CategoryService

create(Characteristic) - Method in class org.molgenis.service.CharacteristicService

create(DataSet) - Method in class org.molgenis.service.DataSetService

create(DateTimeValue) - Method in class org.molgenis.service.DateTimeValueService

create(DateValue) - Method in class org.molgenis.service.DateValueService

create(DecimalValue) - Method in class org.molgenis.service.DecimalValueService

create(EmailValue) - Method in class org.molgenis.service.EmailValueService

create(HtmlValue) - Method in class org.molgenis.service.HtmlValueService

create(HyperlinkValue) - Method in class org.molgenis.service.HyperlinkValueService

create(Individual) - Method in class org.molgenis.service.IndividualService

create(IntValue) - Method in class org.molgenis.service.IntValueService

create(LongValue) - Method in class org.molgenis.service.LongValueService

create(MolgenisFile) - Method in class org.molgenis.service.MolgenisFileService

create(MrefValue) - Method in class org.molgenis.service.MrefValueService

create(ObservableFeature) - Method in class org.molgenis.service.ObservableFeatureService

create(ObservationSet) - Method in class org.molgenis.service.ObservationSetService

create(ObservationTarget) - Method in class org.molgenis.service.ObservationTargetService

create(ObservedValue) - Method in class org.molgenis.service.ObservedValueService

create(Ontology) - Method in class org.molgenis.service.OntologyService

create(OntologyTerm) - Method in class org.molgenis.service.OntologyTermService

create(Panel) - Method in class org.molgenis.service.PanelService

create(PanelSource) - Method in class org.molgenis.service.PanelSourceService

create(Protocol) - Method in class org.molgenis.service.ProtocolService

create(RuntimeProperty) - Method in class org.molgenis.service.RuntimePropertyService

create(Species) - Method in class org.molgenis.service.SpeciesService

create(StringValue) - Method in class org.molgenis.service.StringValueService

create(TextValue) - Method in class org.molgenis.service.TextValueService

create(Value) - Method in class org.molgenis.service.ValueService

create(XrefValue) - Method in class org.molgenis.service.XrefValueService

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

createList(int) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

Return EMPTY list of given allocated size

CURRENTPANEL - Static variable in class org.molgenis.omx.observ.target.PanelSource

CURRENTPANEL_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.PanelSource

D

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

DataSet(DataSet) - Constructor for class org.molgenis.omx.observ.DataSet

copy constructor

DataSetEntityImporter - Class in org.molgenis.omx.observ.db

Reads DataSet from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

DataSetEntityImporter() - Constructor for class org.molgenis.omx.observ.db.DataSetEntityImporter

DataSetForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity DataSet

DataSetForm() - Constructor for class org.molgenis.omx.observ.ui.DataSetForm

DataSetForm(DataSet) - Constructor for class org.molgenis.omx.observ.ui.DataSetForm

DataSetJpaMapper - Class in org.molgenis.omx.observ.db

DataSetJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.DataSetJpaMapper

DataSetService - Class in org.molgenis.service

DataSetService() - Constructor for class org.molgenis.service.DataSetService

DataSetTable - Class in org.molgenis.omx.dataset

DataSetTable If this table is too slow consider creating database an index on the ObservedValue table : One on the fields Feature-Value and one on ObservationSet-Feature-Value

DataSetTable(DataSet, Database) - Constructor for class org.molgenis.omx.dataset.DataSetTable

DataSetTableIterator - Class in org.molgenis.omx.dataset

DataSetTableIterator(Database, List<Field>, Query<ObservationSet>) - Constructor for class org.molgenis.omx.dataset.DataSetTableIterator

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

DateTimeValue(DateTimeValue) - Constructor for class org.molgenis.omx.observ.value.DateTimeValue

copy constructor

DateTimeValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads DateTimeValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

DateTimeValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.DateTimeValueEntityImporter

DateTimeValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity DateTimeValue

DateTimeValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.DateTimeValueForm

DateTimeValueForm(DateTimeValue) - Constructor for class org.molgenis.omx.observ.value.ui.DateTimeValueForm

DateTimeValueJpaMapper - Class in org.molgenis.omx.observ.value.db

DateTimeValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

DateTimeValueService - Class in org.molgenis.service

DateTimeValueService() - Constructor for class org.molgenis.service.DateTimeValueService

DateValue - Class in org.molgenis.omx.observ.value

DateValue: .

DateValue() - Constructor for class org.molgenis.omx.observ.value.DateValue

DateValue(DateValue) - Constructor for class org.molgenis.omx.observ.value.DateValue

copy constructor

DateValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads DateValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

DateValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.DateValueEntityImporter

DateValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity DateValue

DateValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.DateValueForm

DateValueForm(DateValue) - Constructor for class org.molgenis.omx.observ.value.ui.DateValueForm

DateValueJpaMapper - Class in org.molgenis.omx.observ.value.db

DateValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.DateValueJpaMapper

DateValueService - Class in org.molgenis.service

DateValueService() - Constructor for class org.molgenis.service.DateValueService

DecimalValue - Class in org.molgenis.omx.observ.value

DecimalValue: .

DecimalValue() - Constructor for class org.molgenis.omx.observ.value.DecimalValue

DecimalValue(DecimalValue) - Constructor for class org.molgenis.omx.observ.value.DecimalValue

copy constructor

DecimalValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads DecimalValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

DecimalValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.DecimalValueEntityImporter

DecimalValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity DecimalValue

DecimalValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.DecimalValueForm

DecimalValueForm(DecimalValue) - Constructor for class org.molgenis.omx.observ.value.ui.DecimalValueForm

DecimalValueJpaMapper - Class in org.molgenis.omx.observ.value.db

DecimalValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

DecimalValueService - Class in org.molgenis.service

DecimalValueService() - Constructor for class org.molgenis.service.DecimalValueService

DEFINITION - Static variable in class org.molgenis.omx.observ.Category

DEFINITION - Static variable in class org.molgenis.omx.observ.ObservableFeature

DEFINITION - Static variable in class org.molgenis.omx.observ.target.OntologyTerm

DEFINITION_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Category

DEFINITION_IDENTIFIER - Static variable in class org.molgenis.omx.observ.ObservableFeature

deleteById(Integer) - Method in class org.molgenis.service.AccessionService

deleteById(Integer) - Method in class org.molgenis.service.BoolValueService

deleteById(Integer) - Method in class org.molgenis.service.CategoricalValueService

deleteById(Integer) - Method in class org.molgenis.service.CategoryService

deleteById(Integer) - Method in class org.molgenis.service.CharacteristicService

deleteById(Integer) - Method in class org.molgenis.service.DataSetService

deleteById(Integer) - Method in class org.molgenis.service.DateTimeValueService

deleteById(Integer) - Method in class org.molgenis.service.DateValueService

deleteById(Integer) - Method in class org.molgenis.service.DecimalValueService

deleteById(Integer) - Method in class org.molgenis.service.EmailValueService

deleteById(Integer) - Method in class org.molgenis.service.HtmlValueService

deleteById(Integer) - Method in class org.molgenis.service.HyperlinkValueService

deleteById(Integer) - Method in class org.molgenis.service.IndividualService

deleteById(Integer) - Method in class org.molgenis.service.IntValueService

deleteById(Integer) - Method in class org.molgenis.service.LongValueService

deleteById(Integer) - Method in class org.molgenis.service.MolgenisFileService

deleteById(Integer) - Method in class org.molgenis.service.MrefValueService

deleteById(Integer) - Method in class org.molgenis.service.ObservableFeatureService

deleteById(Integer) - Method in class org.molgenis.service.ObservationSetService

deleteById(Integer) - Method in class org.molgenis.service.ObservationTargetService

deleteById(Integer) - Method in class org.molgenis.service.ObservedValueService

deleteById(Integer) - Method in class org.molgenis.service.OntologyService

deleteById(Integer) - Method in class org.molgenis.service.OntologyTermService

deleteById(Integer) - Method in class org.molgenis.service.PanelService

deleteById(Integer) - Method in class org.molgenis.service.PanelSourceService

deleteById(Integer) - Method in class org.molgenis.service.ProtocolService

deleteById(Integer) - Method in class org.molgenis.service.RuntimePropertyService

deleteById(Integer) - Method in class org.molgenis.service.SpeciesService

deleteById(Integer) - Method in class org.molgenis.service.StringValueService

deleteById(Integer) - Method in class org.molgenis.service.TextValueService

deleteById(Integer) - Method in class org.molgenis.service.ValueService

deleteById(Integer) - Method in class org.molgenis.service.XrefValueService

deleteFile(MolgenisFile, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Deletes the file that belongs to this MolgenisFile entity.

deleteFileStorage(Database) - Method in class org.molgenis.omx.services.StorageHandler

Remove file storage location and validation status.

DESCRIPTION - Static variable in class org.molgenis.omx.observ.Characteristic

destroy(MolgenisEntity) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

destroy(MolgenisFile) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

destroy(RuntimeProperty) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

destroy(Category) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

destroy(Characteristic) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

destroy(DataSet) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

destroy(ObservableFeature) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

destroy(ObservationSet) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

destroy(ObservationTarget) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

destroy(ObservedValue) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

destroy(Protocol_Features) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

destroy(Protocol_Subprotocols) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

destroy(Protocol) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

destroy(Accession) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

destroy(Individual) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

destroy(Ontology) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

destroy(OntologyTerm) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

destroy(Panel_Individuals) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

destroy(Panel) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

destroy(PanelSource) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

destroy(Species) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

destroy(BoolValue) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

destroy(CategoricalValue) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

destroy(DateTimeValue) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

destroy(DateValue) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

destroy(DecimalValue) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

destroy(EmailValue) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

destroy(HtmlValue) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

destroy(HyperlinkValue) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

destroy(IntValue) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

destroy(LongValue) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

destroy(MrefValue_Value) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

destroy(MrefValue) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

destroy(StringValue) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

destroy(TextValue) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

destroy(Value) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

destroy(XrefValue) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

displayUsage(PrintWriter, Database) - Method in class org.molgenis.omx.services.FileDownloadService

displayUsage(PrintWriter, Database) - Method in class org.molgenis.omx.services.FileViewService

doUpload(Database, MolgenisFile, File, boolean) - Static method in class org.molgenis.omx.services.FileUploadUtils

Generic file upload.

doUpload(Database, boolean, String, String, File, HashMap<String, String>, boolean) - Static method in class org.molgenis.omx.services.FileUploadUtils

Generic file upload.

E

edit(MolgenisEntity) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

edit(MolgenisFile) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

edit(RuntimeProperty) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

edit(Category) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

edit(Characteristic) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

edit(DataSet) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

edit(ObservableFeature) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

edit(ObservationSet) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

edit(ObservationTarget) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

edit(ObservedValue) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

edit(Protocol_Features) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

edit(Protocol_Subprotocols) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

edit(Protocol) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

edit(Accession) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

edit(Individual) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

edit(Ontology) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

edit(OntologyTerm) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

edit(Panel_Individuals) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

edit(Panel) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

edit(PanelSource) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

edit(Species) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

edit(BoolValue) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

edit(CategoricalValue) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

edit(DateTimeValue) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

edit(DateValue) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

edit(DecimalValue) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

edit(EmailValue) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

edit(HtmlValue) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

edit(HyperlinkValue) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

edit(IntValue) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

edit(LongValue) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

edit(MrefValue_Value) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

edit(MrefValue) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

edit(StringValue) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

edit(TextValue) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

edit(Value) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

edit(XrefValue) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

EmailValue - Class in org.molgenis.omx.observ.value

EmailValue: .

EmailValue() - Constructor for class org.molgenis.omx.observ.value.EmailValue

EmailValue(EmailValue) - Constructor for class org.molgenis.omx.observ.value.EmailValue

copy constructor

EmailValueDecorator<E extends EmailValue> - Class in org.molgenis.omx.decorators

EmailValueDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.decorators.EmailValueDecorator

EmailValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads EmailValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

EmailValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.EmailValueEntityImporter

EmailValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity EmailValue

EmailValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.EmailValueForm

EmailValueForm(EmailValue) - Constructor for class org.molgenis.omx.observ.value.ui.EmailValueForm

EmailValueJpaMapper - Class in org.molgenis.omx.observ.value.db

EmailValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

EmailValueService - Class in org.molgenis.service

EmailValueService() - Constructor for class org.molgenis.service.EmailValueService

emptyAndAddToCart(ShoppingCartController.FeaturesRequest) - Method in class org.molgenis.omx.cart.ShoppingCartController

emptyCart() - Method in class org.molgenis.omx.cart.ShoppingCartController

ENDTIME - Static variable in class org.molgenis.omx.observ.DataSet

equals(Object) - Method in class org.molgenis.omx.core.MolgenisEntity

equals(Object) - Method in class org.molgenis.omx.core.MolgenisFile

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.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_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.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.

executeAdd(List<? extends MolgenisEntity>) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

executeAdd(List<? extends MolgenisFile>) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

executeAdd(List<? extends RuntimeProperty>) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

executeAdd(List<? extends Category>) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

executeAdd(List<? extends Characteristic>) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

executeAdd(List<? extends DataSet>) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

executeAdd(List<? extends ObservableFeature>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

executeAdd(List<? extends ObservationSet>) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

executeAdd(List<? extends ObservationTarget>) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

executeAdd(List<? extends ObservedValue>) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

executeAdd(List<? extends Protocol_Features>) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

executeAdd(List<? extends Protocol_Subprotocols>) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

executeAdd(List<? extends Protocol>) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

executeAdd(List<? extends Accession>) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

executeAdd(List<? extends Individual>) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

executeAdd(List<? extends Ontology>) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

executeAdd(List<? extends OntologyTerm>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

executeAdd(List<? extends Panel_Individuals>) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

executeAdd(List<? extends Panel>) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

executeAdd(List<? extends PanelSource>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

executeAdd(List<? extends Species>) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

executeAdd(List<? extends BoolValue>) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

executeAdd(List<? extends CategoricalValue>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

executeAdd(List<? extends DateTimeValue>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

executeAdd(List<? extends DateValue>) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

executeAdd(List<? extends DecimalValue>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

executeAdd(List<? extends EmailValue>) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

executeAdd(List<? extends HtmlValue>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

executeAdd(List<? extends HyperlinkValue>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

executeAdd(List<? extends IntValue>) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

executeAdd(List<? extends LongValue>) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

executeAdd(List<? extends MrefValue_Value>) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

executeAdd(List<? extends MrefValue>) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

executeAdd(List<? extends StringValue>) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

executeAdd(List<? extends TextValue>) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

executeAdd(List<? extends Value>) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

executeAdd(List<? extends XrefValue>) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

executeRemove(List<? extends MolgenisEntity>) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

executeRemove(List<? extends MolgenisFile>) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

executeRemove(List<? extends RuntimeProperty>) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

executeRemove(List<? extends Category>) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

executeRemove(List<? extends Characteristic>) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

executeRemove(List<? extends DataSet>) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

executeRemove(List<? extends ObservableFeature>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

executeRemove(List<? extends ObservationSet>) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

executeRemove(List<? extends ObservationTarget>) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

executeRemove(List<? extends ObservedValue>) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

executeRemove(List<? extends Protocol_Features>) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

executeRemove(List<? extends Protocol_Subprotocols>) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

executeRemove(List<? extends Protocol>) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

executeRemove(List<? extends Accession>) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

executeRemove(List<? extends Individual>) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

executeRemove(List<? extends Ontology>) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

executeRemove(List<? extends OntologyTerm>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

executeRemove(List<? extends Panel_Individuals>) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

executeRemove(List<? extends Panel>) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

executeRemove(List<? extends PanelSource>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

executeRemove(List<? extends Species>) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

executeRemove(List<? extends BoolValue>) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

executeRemove(List<? extends CategoricalValue>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

executeRemove(List<? extends DateTimeValue>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

executeRemove(List<? extends DateValue>) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

executeRemove(List<? extends DecimalValue>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

executeRemove(List<? extends EmailValue>) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

executeRemove(List<? extends HtmlValue>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

executeRemove(List<? extends HyperlinkValue>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

executeRemove(List<? extends IntValue>) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

executeRemove(List<? extends LongValue>) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

executeRemove(List<? extends MrefValue_Value>) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

executeRemove(List<? extends MrefValue>) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

executeRemove(List<? extends StringValue>) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

executeRemove(List<? extends TextValue>) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

executeRemove(List<? extends Value>) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

executeRemove(List<? extends XrefValue>) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

executeUpdate(List<? extends MolgenisEntity>) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

executeUpdate(List<? extends MolgenisFile>) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

executeUpdate(List<? extends RuntimeProperty>) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

executeUpdate(List<? extends Category>) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

executeUpdate(List<? extends Characteristic>) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

executeUpdate(List<? extends DataSet>) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

executeUpdate(List<? extends ObservableFeature>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

executeUpdate(List<? extends ObservationSet>) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

executeUpdate(List<? extends ObservationTarget>) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

executeUpdate(List<? extends ObservedValue>) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

executeUpdate(List<? extends Protocol_Features>) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

executeUpdate(List<? extends Protocol_Subprotocols>) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

executeUpdate(List<? extends Protocol>) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

executeUpdate(List<? extends Accession>) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

executeUpdate(List<? extends Individual>) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

executeUpdate(List<? extends Ontology>) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

executeUpdate(List<? extends OntologyTerm>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

executeUpdate(List<? extends Panel_Individuals>) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

executeUpdate(List<? extends Panel>) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

executeUpdate(List<? extends PanelSource>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

executeUpdate(List<? extends Species>) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

executeUpdate(List<? extends BoolValue>) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

executeUpdate(List<? extends CategoricalValue>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

executeUpdate(List<? extends DateTimeValue>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

executeUpdate(List<? extends DateValue>) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

executeUpdate(List<? extends DecimalValue>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

executeUpdate(List<? extends EmailValue>) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

executeUpdate(List<? extends HtmlValue>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

executeUpdate(List<? extends HyperlinkValue>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

executeUpdate(List<? extends IntValue>) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

executeUpdate(List<? extends LongValue>) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

executeUpdate(List<? extends MrefValue_Value>) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

executeUpdate(List<? extends MrefValue>) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

executeUpdate(List<? extends StringValue>) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

executeUpdate(List<? extends TextValue>) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

executeUpdate(List<? extends Value>) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

executeUpdate(List<? extends XrefValue>) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

EXTENSION - Static variable in class org.molgenis.omx.core.MolgenisFile

F

FATHER - Static variable in class org.molgenis.omx.observ.target.Individual

FATHER_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Individual

FEATURE - Static variable in class org.molgenis.omx.observ.ObservedValue

FEATURE_IDENTIFIER - 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

FEATURES_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol

FEATURES_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol_Features

FileDownloadService - Class in org.molgenis.omx.services

FileDownloadService(MolgenisContext) - Constructor for class org.molgenis.omx.services.FileDownloadService

fileNameChecks(String) - Static method in class org.molgenis.omx.services.FileUploadUtils

FileUploadService - Class in org.molgenis.omx.services

FileUploadService(MolgenisContext) - Constructor for class org.molgenis.omx.services.FileUploadService

FileUploadUtils - Class in org.molgenis.omx.services

FileUploadUtils() - Constructor for class org.molgenis.omx.services.FileUploadUtils

FileViewService - Class in org.molgenis.omx.services

FileViewService(MolgenisContext) - Constructor for class org.molgenis.omx.services.FileViewService

find(Database, QueryRule...) - Static method in class org.molgenis.omx.core.MolgenisEntity

Shorthand for db.find(MolgenisEntity.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.core.MolgenisFile

Shorthand for db.find(MolgenisFile.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.core.RuntimeProperty

Shorthand for db.find(RuntimeProperty.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.Category

Shorthand for db.find(Category.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.Characteristic

Shorthand for db.find(Characteristic.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.DataSet

Shorthand for db.find(DataSet.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.ObservableFeature

Shorthand for db.find(ObservableFeature.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.ObservationSet

Shorthand for db.find(ObservationSet.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.ObservationTarget

Shorthand for db.find(ObservationTarget.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.ObservedValue

Shorthand for db.find(ObservedValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.Protocol

Shorthand for db.find(Protocol.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.Protocol_Features

Shorthand for db.find(Protocol_Features.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.Protocol_Subprotocols

Shorthand for db.find(Protocol_Subprotocols.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Accession

Shorthand for db.find(Accession.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Individual

Shorthand for db.find(Individual.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Ontology

Shorthand for db.find(Ontology.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.OntologyTerm

Shorthand for db.find(OntologyTerm.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Panel

Shorthand for db.find(Panel.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Panel_Individuals

Shorthand for db.find(Panel_Individuals.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.PanelSource

Shorthand for db.find(PanelSource.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.target.Species

Shorthand for db.find(Species.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.BoolValue

Shorthand for db.find(BoolValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.CategoricalValue

Shorthand for db.find(CategoricalValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.DateTimeValue

Shorthand for db.find(DateTimeValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.DateValue

Shorthand for db.find(DateValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.DecimalValue

Shorthand for db.find(DecimalValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.EmailValue

Shorthand for db.find(EmailValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.HtmlValue

Shorthand for db.find(HtmlValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.HyperlinkValue

Shorthand for db.find(HyperlinkValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.IntValue

Shorthand for db.find(IntValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.LongValue

Shorthand for db.find(LongValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.MrefValue

Shorthand for db.find(MrefValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.MrefValue_Value

Shorthand for db.find(MrefValue_Value.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.StringValue

Shorthand for db.find(StringValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.TextValue

Shorthand for db.find(TextValue.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.Value

Shorthand for db.find(Value.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.observ.value.XrefValue

Shorthand for db.find(XrefValue.class, org.molgenis.framework.db.QueryRule ...

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.observ.Protocol_Features

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.observ.Protocol_Subprotocols

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Panel_Individuals

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.observ.value.MrefValue_Value

findByClassName(Database, String) - Static method in class org.molgenis.omx.core.MolgenisEntity

findByFeaturesProtocol(Database, Integer, Integer) - Static method in class org.molgenis.omx.observ.Protocol_Features

findById(Database, Integer) - Static method in class org.molgenis.omx.core.MolgenisEntity

findById(Database, Integer) - Static method in class org.molgenis.omx.core.MolgenisFile

findById(Database, Integer) - Static method in class org.molgenis.omx.core.RuntimeProperty

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.Category

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.Characteristic

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.DataSet

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.ObservableFeature

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.ObservationSet

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.ObservationTarget

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.ObservedValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.Protocol

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Accession

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Individual

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Ontology

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.OntologyTerm

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Panel

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.PanelSource

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.target.Species

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.BoolValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.CategoricalValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.DateTimeValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.DateValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.DecimalValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.EmailValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.HtmlValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.HyperlinkValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.IntValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.LongValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.MrefValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.StringValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.TextValue

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.Value

findById(Database, Integer) - Static method in class org.molgenis.omx.observ.value.XrefValue

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.core.MolgenisFile

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.core.RuntimeProperty

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.Category

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.Characteristic

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.DataSet

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.ObservableFeature

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.ObservationTarget

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.Protocol

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.Accession

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.Individual

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.Ontology

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.OntologyTerm

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.Panel

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.observ.target.Species

findByIndividualsPanel(Database, Integer, Integer) - Static method in class org.molgenis.omx.observ.target.Panel_Individuals

findByName(Database, String) - Static method in class org.molgenis.omx.core.MolgenisFile

findByName(Database, String) - Static method in class org.molgenis.omx.core.RuntimeProperty

findByNameType(Database, String, String) - Static method in class org.molgenis.omx.core.MolgenisEntity

findByOntologyTermAccession(Database, Integer, String) - Static method in class org.molgenis.omx.observ.target.Accession

findByOntologyTermAccession(Database, Integer, String) - Static method in class org.molgenis.omx.observ.target.OntologyTerm

findByOntologyTermAccession(Database, Integer, String) - Static method in class org.molgenis.omx.observ.target.Species

findByPartOfDataSetTime(Database, Integer, Date) - Static method in class org.molgenis.omx.observ.ObservationSet

findBySubprotocolsProtocol(Database, Integer, Integer) - Static method in class org.molgenis.omx.observ.Protocol_Subprotocols

findByValueMrefValue(Database, Integer, Integer) - Static method in class org.molgenis.omx.observ.value.MrefValue_Value

findFile(MolgenisFile, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Find the type of MolgenisFile (subclass) for this file, if it exists.

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToBoolValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToCategoricalValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToDateTimeValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToDateValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToDecimalValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToEmailValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToHtmlValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToHyperlinkValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToIntValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToLongValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToMrefValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToStringValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToTextValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in interface org.molgenis.omx.converters.TupleToValueConverter

Converts a tuple column value to a value entity

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.TupleToXrefValueConverter

fromTuple(Tuple, String, ObservableFeature) - Method in class org.molgenis.omx.converters.ValueConverter

G

genericAddUpdateChecks(List<E>) - Method in class org.molgenis.omx.decorators.MolgenisFileDecorator

get(String) - Method in class org.molgenis.omx.core.MolgenisEntity

Generic getter.

get(String) - Method in class org.molgenis.omx.core.MolgenisFile

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.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_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(Database) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

get__Type() - Method in class org.molgenis.omx.observ.value.Value

Get the Subtypes have to be set to allow searching.

get__Type(Database) - Method in class org.molgenis.omx.observ.value.Value

Deprecated.

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.

getAllColumns() - Method in class org.molgenis.omx.dataset.DataSetTable

getAllColumns() - Method in class org.molgenis.omx.protocol.ProtocolTable

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_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.

getCart() - Method in class org.molgenis.omx.cart.ShoppingCartController

getClassName() - Method in class org.molgenis.omx.core.MolgenisEntity

Get the Full name of the entity.

getClassName(Database) - Method in class org.molgenis.omx.core.MolgenisEntity

Deprecated.

getCount() - Method in class org.molgenis.omx.dataset.DataSetTable

getCount() - Method in class org.molgenis.omx.protocol.ProtocolTable

Count the number of protocols and features of this protocol (excluding this protocol itself)

getCurrentPanel() - Method in class org.molgenis.omx.observ.target.PanelSource

Get the Panel for which these sources are defined..

getCurrentPanel(Database) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getCurrentPanel_Id() - Method in class org.molgenis.omx.observ.target.PanelSource

getCurrentPanel_Identifier() - Method in class org.molgenis.omx.observ.target.PanelSource

Get a pretty label Identifier for cross reference CurrentPanel to Panel.Id.

getDataSet() - Method in class org.molgenis.omx.dataset.DataSetTable

getDataType() - Method in class org.molgenis.omx.observ.ObservableFeature

Get the (Optional) Reference to the technical data type.

getDataType(Database) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

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.

getDb() - Method in class org.molgenis.omx.dataset.DataSetTable

getDb() - Method in class org.molgenis.omx.protocol.ProtocolTable

getDefinition() - Method in class org.molgenis.omx.observ.Category

Get the The category that is being measured in a specific way..

getDefinition(Database) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getDefinition() - Method in class org.molgenis.omx.observ.ObservableFeature

Get the The concept that is being measured in a specific way..

getDefinition(Database) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

getDefinition() - Method in class org.molgenis.omx.observ.target.OntologyTerm

Get the (Optional) The definition of the term..

getDefinition(Database) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Deprecated.

getDefinition_Id() - Method in class org.molgenis.omx.observ.Category

getDefinition_Id() - Method in class org.molgenis.omx.observ.ObservableFeature

getDefinition_Identifier() - Method in class org.molgenis.omx.observ.Category

Get a pretty label Identifier for cross reference Definition to OntologyTerm.Id.

getDefinition_Identifier() - Method in class org.molgenis.omx.observ.ObservableFeature

Get a pretty label Identifier for cross reference Definition to OntologyTerm.Id.

getDescription() - Method in class org.molgenis.omx.observ.Characteristic

Get the (Optional) Rudimentary meta data about the observable feature.

getDescription(Database) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

getEndTime() - Method in class org.molgenis.omx.observ.DataSet

Get the (Optional) time when the protocol ended..

getEndTime(Database) - Method in class org.molgenis.omx.observ.DataSet

Deprecated.

getEntity() - Method in class org.molgenis.service.AccessionService

getEntity() - Method in class org.molgenis.service.BoolValueService

getEntity() - Method in class org.molgenis.service.CategoricalValueService

getEntity() - Method in class org.molgenis.service.CategoryService

getEntity() - Method in class org.molgenis.service.CharacteristicService

getEntity() - Method in class org.molgenis.service.DataSetService

getEntity() - Method in class org.molgenis.service.DateTimeValueService

getEntity() - Method in class org.molgenis.service.DateValueService

getEntity() - Method in class org.molgenis.service.DecimalValueService

getEntity() - Method in class org.molgenis.service.EmailValueService

getEntity() - Method in class org.molgenis.service.HtmlValueService

getEntity() - Method in class org.molgenis.service.HyperlinkValueService

getEntity() - Method in class org.molgenis.service.IndividualService

getEntity() - Method in class org.molgenis.service.IntValueService

getEntity() - Method in class org.molgenis.service.LongValueService

getEntity() - Method in class org.molgenis.service.MolgenisFileService

getEntity() - Method in class org.molgenis.service.MrefValueService

getEntity() - Method in class org.molgenis.service.ObservableFeatureService

getEntity() - Method in class org.molgenis.service.ObservationSetService

getEntity() - Method in class org.molgenis.service.ObservationTargetService

getEntity() - Method in class org.molgenis.service.ObservedValueService

getEntity() - Method in class org.molgenis.service.OntologyService

getEntity() - Method in class org.molgenis.service.OntologyTermService

getEntity() - Method in class org.molgenis.service.PanelService

getEntity() - Method in class org.molgenis.service.PanelSourceService

getEntity() - Method in class org.molgenis.service.ProtocolService

getEntity() - Method in class org.molgenis.service.RuntimePropertyService

getEntity() - Method in class org.molgenis.service.SpeciesService

getEntity() - Method in class org.molgenis.service.StringValueService

getEntity() - Method in class org.molgenis.service.TextValueService

getEntity() - Method in class org.molgenis.service.ValueService

getEntity() - Method in class org.molgenis.service.XrefValueService

getEntityClass() - Method in class org.molgenis.omx.core.ui.MolgenisEntityForm

getEntityClass() - Method in class org.molgenis.omx.core.ui.MolgenisFileForm

getEntityClass() - Method in class org.molgenis.omx.core.ui.RuntimePropertyForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.AccessionForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.IndividualForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.OntologyForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.OntologyTermForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.Panel_IndividualsForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.PanelForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.PanelSourceForm

getEntityClass() - Method in class org.molgenis.omx.observ.target.ui.SpeciesForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.CategoryForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.CharacteristicForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.DataSetForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.ObservableFeatureForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.ObservationSetForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.ObservationTargetForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.ObservedValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.Protocol_FeaturesForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.Protocol_SubprotocolsForm

getEntityClass() - Method in class org.molgenis.omx.observ.ui.ProtocolForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.BoolValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.CategoricalValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.DateTimeValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.DateValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.DecimalValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.EmailValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.HtmlValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.HyperlinkValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.IntValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.LongValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.MrefValue_ValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.MrefValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.StringValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.TextValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.ValueForm

getEntityClass() - Method in class org.molgenis.omx.observ.value.ui.XrefValueForm

getExtension() - Method in class org.molgenis.omx.core.MolgenisFile

Get the The file extension.

getExtension(Database) - Method in class org.molgenis.omx.core.MolgenisFile

Deprecated.

getFather() - Method in class org.molgenis.omx.observ.target.Individual

Get the Refers to the father of the individual..

getFather(Database) - Method in class org.molgenis.omx.observ.target.Individual

Deprecated.

getFather_Id() - Method in class org.molgenis.omx.observ.target.Individual

getFather_Identifier() - Method in class org.molgenis.omx.observ.target.Individual

Get a pretty label Identifier for cross reference Father to Individual.Id.

getFeature() - Method in class org.molgenis.omx.observ.ObservedValue

Get the References the ObservableFeature that this observation was made on.

getFeature(Database) - Method in class org.molgenis.omx.observ.ObservedValue

Deprecated.

getFeature_Id() - Method in class org.molgenis.omx.observ.ObservedValue

getFeature_Identifier() - Method in class org.molgenis.omx.observ.ObservedValue

Get a pretty label Identifier for cross reference Feature to ObservableFeature.Id.

getFeatures() - Method in class org.molgenis.omx.observ.Protocol

Get the parameters (in/out) that are used or produced by this protocol..

getFeatures(Database) - Method in class org.molgenis.omx.observ.Protocol

Deprecated.

getFeatures() - Method in class org.molgenis.omx.observ.Protocol_Features

Get the .

getFeatures(Database) - Method in class org.molgenis.omx.observ.Protocol_Features

Deprecated.

getFeatures_Id() - Method in class org.molgenis.omx.observ.Protocol

getFeatures_Id() - Method in class org.molgenis.omx.observ.Protocol_Features

getFeatures_Identifier() - Method in class org.molgenis.omx.observ.Protocol

Get a pretty label for cross reference Features to ObservableFeature.Id.

getFeatures_Identifier() - Method in class org.molgenis.omx.observ.Protocol_Features

Get a pretty label Identifier for cross reference Features to ObservableFeature.Id.

getFeaturesProtocolCollection() - Method in class org.molgenis.omx.observ.ObservableFeature

getFeaturesProtocolCollection(Database) - Method in class org.molgenis.omx.observ.ObservableFeature

getFields(boolean) - Method in class org.molgenis.omx.core.MolgenisEntity

Get the names of all public properties of MolgenisEntity.

getFields() - Method in class org.molgenis.omx.core.MolgenisEntity

getFields(String) - Method in class org.molgenis.omx.core.MolgenisEntity

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.core.MolgenisFile

Get the names of all public properties of MolgenisFile.

getFields() - Method in class org.molgenis.omx.core.MolgenisFile

getFields(String) - Method in class org.molgenis.omx.core.MolgenisFile

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.core.RuntimeProperty

Get the names of all public properties of RuntimeProperty.

getFields() - Method in class org.molgenis.omx.core.RuntimeProperty

getFields(String) - Method in class org.molgenis.omx.core.RuntimeProperty

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.Category

Get the names of all public properties of Category.

getFields() - Method in class org.molgenis.omx.observ.Category

getFields(String) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.Characteristic

Get the names of all public properties of Characteristic.

getFields() - Method in class org.molgenis.omx.observ.Characteristic

getFields(String) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.DataSet

Get the names of all public properties of DataSet.

getFields() - Method in class org.molgenis.omx.observ.DataSet

getFields(String) - Method in class org.molgenis.omx.observ.DataSet

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.ObservableFeature

Get the names of all public properties of ObservableFeature.

getFields() - Method in class org.molgenis.omx.observ.ObservableFeature

getFields(String) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.ObservationSet

Get the names of all public properties of ObservationSet.

getFields() - Method in class org.molgenis.omx.observ.ObservationSet

getFields(String) - Method in class org.molgenis.omx.observ.ObservationSet

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.ObservationTarget

Get the names of all public properties of ObservationTarget.

getFields() - Method in class org.molgenis.omx.observ.ObservationTarget

getFields(String) - Method in class org.molgenis.omx.observ.ObservationTarget

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.ObservedValue

Get the names of all public properties of ObservedValue.

getFields() - Method in class org.molgenis.omx.observ.ObservedValue

getFields(String) - Method in class org.molgenis.omx.observ.ObservedValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.Protocol

Get the names of all public properties of Protocol.

getFields() - Method in class org.molgenis.omx.observ.Protocol

getFields(String) - Method in class org.molgenis.omx.observ.Protocol

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.Protocol_Features

Get the names of all public properties of Protocol_Features.

getFields() - Method in class org.molgenis.omx.observ.Protocol_Features

getFields(String) - Method in class org.molgenis.omx.observ.Protocol_Features

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Get the names of all public properties of Protocol_Subprotocols.

getFields() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getFields(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Accession

Get the names of all public properties of Accession.

getFields() - Method in class org.molgenis.omx.observ.target.Accession

getFields(String) - Method in class org.molgenis.omx.observ.target.Accession

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Individual

Get the names of all public properties of Individual.

getFields() - Method in class org.molgenis.omx.observ.target.Individual

getFields(String) - Method in class org.molgenis.omx.observ.target.Individual

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Ontology

Get the names of all public properties of Ontology.

getFields() - Method in class org.molgenis.omx.observ.target.Ontology

getFields(String) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Get the names of all public properties of OntologyTerm.

getFields() - Method in class org.molgenis.omx.observ.target.OntologyTerm

getFields(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Panel

Get the names of all public properties of Panel.

getFields() - Method in class org.molgenis.omx.observ.target.Panel

getFields(String) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Get the names of all public properties of Panel_Individuals.

getFields() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getFields(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.PanelSource

Get the names of all public properties of PanelSource.

getFields() - Method in class org.molgenis.omx.observ.target.PanelSource

getFields(String) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.target.Species

Get the names of all public properties of Species.

getFields() - Method in class org.molgenis.omx.observ.target.Species

getFields(String) - Method in class org.molgenis.omx.observ.target.Species

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.BoolValue

Get the names of all public properties of BoolValue.

getFields() - Method in class org.molgenis.omx.observ.value.BoolValue

getFields(String) - Method in class org.molgenis.omx.observ.value.BoolValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Get the names of all public properties of CategoricalValue.

getFields() - Method in class org.molgenis.omx.observ.value.CategoricalValue

getFields(String) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.DateTimeValue

Get the names of all public properties of DateTimeValue.

getFields() - Method in class org.molgenis.omx.observ.value.DateTimeValue

getFields(String) - Method in class org.molgenis.omx.observ.value.DateTimeValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.DateValue

Get the names of all public properties of DateValue.

getFields() - Method in class org.molgenis.omx.observ.value.DateValue

getFields(String) - Method in class org.molgenis.omx.observ.value.DateValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.DecimalValue

Get the names of all public properties of DecimalValue.

getFields() - Method in class org.molgenis.omx.observ.value.DecimalValue

getFields(String) - Method in class org.molgenis.omx.observ.value.DecimalValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.EmailValue

Get the names of all public properties of EmailValue.

getFields() - Method in class org.molgenis.omx.observ.value.EmailValue

getFields(String) - Method in class org.molgenis.omx.observ.value.EmailValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.HtmlValue

Get the names of all public properties of HtmlValue.

getFields() - Method in class org.molgenis.omx.observ.value.HtmlValue

getFields(String) - Method in class org.molgenis.omx.observ.value.HtmlValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Get the names of all public properties of HyperlinkValue.

getFields() - Method in class org.molgenis.omx.observ.value.HyperlinkValue

getFields(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.IntValue

Get the names of all public properties of IntValue.

getFields() - Method in class org.molgenis.omx.observ.value.IntValue

getFields(String) - Method in class org.molgenis.omx.observ.value.IntValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.LongValue

Get the names of all public properties of LongValue.

getFields() - Method in class org.molgenis.omx.observ.value.LongValue

getFields(String) - Method in class org.molgenis.omx.observ.value.LongValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.MrefValue

Get the names of all public properties of MrefValue.

getFields() - Method in class org.molgenis.omx.observ.value.MrefValue

getFields(String) - Method in class org.molgenis.omx.observ.value.MrefValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Get the names of all public properties of MrefValue_Value.

getFields() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

getFields(String) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.StringValue

Get the names of all public properties of StringValue.

getFields() - Method in class org.molgenis.omx.observ.value.StringValue

getFields(String) - Method in class org.molgenis.omx.observ.value.StringValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.TextValue

Get the names of all public properties of TextValue.

getFields() - Method in class org.molgenis.omx.observ.value.TextValue

getFields(String) - Method in class org.molgenis.omx.observ.value.TextValue

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.Value

Get the names of all public properties of Value.

getFields() - Method in class org.molgenis.omx.observ.value.Value

getFields(String) - Method in class org.molgenis.omx.observ.value.Value

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.observ.value.XrefValue

Get the names of all public properties of XrefValue.

getFields() - Method in class org.molgenis.omx.observ.value.XrefValue

getFields(String) - Method in class org.molgenis.omx.observ.value.XrefValue

Deprecated.

getFieldType(String) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

getFile(MolgenisFile, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Get the file pointer for this MolgenisFile, if it exists.

getFile(String, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Get the file pointer for this name of a MolgenisFile, if it exists.

getFileDirectly(String, String, String, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Get the file pointer for this filename / extension / type, bypassing MolgenisFile to handle it.

getFileStorage() - Method in class org.molgenis.omx.services.Report

getFileStorage(Database) - Method in class org.molgenis.omx.services.StorageHandler

Get the path of the file storage, regardless whether it is valid or not.

getFileStorage(boolean, Database) - Method in class org.molgenis.omx.services.StorageHandler

Get the path of the file storage.

getFileStoragePropsPresent() - Method in class org.molgenis.omx.services.Report

getFolderExists() - Method in class org.molgenis.omx.services.Report

getFolderHasContent() - Method in class org.molgenis.omx.services.Report

getHeaders() - Method in class org.molgenis.omx.core.ui.MolgenisEntityForm

getHeaders() - Method in class org.molgenis.omx.core.ui.MolgenisFileForm

getHeaders() - Method in class org.molgenis.omx.core.ui.RuntimePropertyForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.AccessionForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.IndividualForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.OntologyForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.OntologyTermForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.Panel_IndividualsForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.PanelForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.PanelSourceForm

getHeaders() - Method in class org.molgenis.omx.observ.target.ui.SpeciesForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.CategoryForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.CharacteristicForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.DataSetForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.ObservableFeatureForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.ObservationSetForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.ObservationTargetForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.ObservedValueForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.Protocol_FeaturesForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.Protocol_SubprotocolsForm

getHeaders() - Method in class org.molgenis.omx.observ.ui.ProtocolForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.BoolValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.CategoricalValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.DateTimeValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.DateValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.DecimalValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.EmailValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.HtmlValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.HyperlinkValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.IntValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.LongValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.MrefValue_ValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.MrefValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.StringValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.TextValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.ValueForm

getHeaders() - Method in class org.molgenis.omx.observ.value.ui.XrefValueForm

getId() - Method in interface org.molgenis.omx.core.Autoid

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.MolgenisFile

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..

getIdentifier() - Method in interface org.molgenis.omx.core.Identifiable

getIdentifier() - Method in class org.molgenis.omx.core.MolgenisFile

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

getIdentifier(Database) - Method in class org.molgenis.omx.core.MolgenisFile

Deprecated.

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(Database) - Method in class org.molgenis.omx.core.RuntimeProperty

Deprecated.

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(Database) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

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.

getIdentifier(Database) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getIdField() - Method in class org.molgenis.omx.core.MolgenisEntity

getIdField() - Method in class org.molgenis.omx.core.MolgenisFile

getIdField() - Method in class org.molgenis.omx.core.RuntimeProperty

getIdField() - Method in class org.molgenis.omx.observ.Category

getIdField() - Method in class org.molgenis.omx.observ.Characteristic

getIdField() - Method in class org.molgenis.omx.observ.DataSet

getIdField() - Method in class org.molgenis.omx.observ.ObservableFeature

getIdField() - Method in class org.molgenis.omx.observ.ObservationSet

getIdField() - Method in class org.molgenis.omx.observ.ObservationTarget

getIdField() - Method in class org.molgenis.omx.observ.ObservedValue

getIdField() - Method in class org.molgenis.omx.observ.Protocol

getIdField() - Method in class org.molgenis.omx.observ.Protocol_Features

getIdField() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getIdField() - Method in class org.molgenis.omx.observ.target.Accession

getIdField() - Method in class org.molgenis.omx.observ.target.Individual

getIdField() - Method in class org.molgenis.omx.observ.target.Ontology

getIdField() - Method in class org.molgenis.omx.observ.target.OntologyTerm

getIdField() - Method in class org.molgenis.omx.observ.target.Panel

getIdField() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getIdField() - Method in class org.molgenis.omx.observ.target.PanelSource

getIdField() - Method in class org.molgenis.omx.observ.target.Species

getIdField() - Method in class org.molgenis.omx.observ.value.BoolValue

getIdField() - Method in class org.molgenis.omx.observ.value.CategoricalValue

getIdField() - Method in class org.molgenis.omx.observ.value.DateTimeValue

getIdField() - Method in class org.molgenis.omx.observ.value.DateValue

getIdField() - Method in class org.molgenis.omx.observ.value.DecimalValue

getIdField() - Method in class org.molgenis.omx.observ.value.EmailValue

getIdField() - Method in class org.molgenis.omx.observ.value.HtmlValue

getIdField() - Method in class org.molgenis.omx.observ.value.HyperlinkValue

getIdField() - Method in class org.molgenis.omx.observ.value.IntValue

getIdField() - Method in class org.molgenis.omx.observ.value.LongValue

getIdField() - Method in class org.molgenis.omx.observ.value.MrefValue

getIdField() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

getIdField() - Method in class org.molgenis.omx.observ.value.StringValue

getIdField() - Method in class org.molgenis.omx.observ.value.TextValue

getIdField() - Method in class org.molgenis.omx.observ.value.Value

getIdField() - Method in class org.molgenis.omx.observ.value.XrefValue

getIdValue() - Method in class org.molgenis.omx.core.MolgenisEntity

getIdValue() - Method in class org.molgenis.omx.core.MolgenisFile

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.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_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(Database) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getIndividuals() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Get the .

getIndividuals(Database) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Deprecated.

getIndividuals_Id() - Method in class org.molgenis.omx.observ.target.Panel

getIndividuals_Id() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getIndividuals_Identifier() - Method in class org.molgenis.omx.observ.target.Panel

Get a pretty label for cross reference Individuals to Individual.Id.

getIndividuals_Identifier() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Get a pretty label Identifier for cross reference Individuals to Individual.Id.

getIndividualsPanelCollection() - Method in class org.molgenis.omx.observ.target.Individual

getIndividualsPanelCollection(Database) - Method in class org.molgenis.omx.observ.target.Individual

getInputs() - Method in class org.molgenis.omx.core.ui.MolgenisEntityForm

getInputs() - Method in class org.molgenis.omx.core.ui.MolgenisFileForm

getInputs() - Method in class org.molgenis.omx.core.ui.RuntimePropertyForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.AccessionForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.IndividualForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.OntologyForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.OntologyTermForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.Panel_IndividualsForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.PanelForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.PanelSourceForm

getInputs() - Method in class org.molgenis.omx.observ.target.ui.SpeciesForm

getInputs() - Method in class org.molgenis.omx.observ.ui.CategoryForm

getInputs() - Method in class org.molgenis.omx.observ.ui.CharacteristicForm

getInputs() - Method in class org.molgenis.omx.observ.ui.DataSetForm

getInputs() - Method in class org.molgenis.omx.observ.ui.ObservableFeatureForm

getInputs() - Method in class org.molgenis.omx.observ.ui.ObservationSetForm

getInputs() - Method in class org.molgenis.omx.observ.ui.ObservationTargetForm

getInputs() - Method in class org.molgenis.omx.observ.ui.ObservedValueForm

getInputs() - Method in class org.molgenis.omx.observ.ui.Protocol_FeaturesForm

getInputs() - Method in class org.molgenis.omx.observ.ui.Protocol_SubprotocolsForm

getInputs() - Method in class org.molgenis.omx.observ.ui.ProtocolForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.BoolValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.CategoricalValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.DateTimeValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.DateValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.DecimalValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.EmailValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.HtmlValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.HyperlinkValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.IntValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.LongValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.MrefValue_ValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.MrefValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.StringValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.TextValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.ValueForm

getInputs() - Method in class org.molgenis.omx.observ.value.ui.XrefValueForm

getIsMissing() - Method in class org.molgenis.omx.observ.Category

Get the whether this value should be treated as missing value..

getIsMissing(Database) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getKey() - Method in class org.molgenis.omx.utils.ValueCell

getLabelFields() - Method in class org.molgenis.omx.core.MolgenisEntity

getLabelFields() - Method in class org.molgenis.omx.core.MolgenisFile

getLabelFields() - Method in class org.molgenis.omx.core.RuntimeProperty

getLabelFields() - Method in class org.molgenis.omx.observ.Category

getLabelFields() - Method in class org.molgenis.omx.observ.Characteristic

getLabelFields() - Method in class org.molgenis.omx.observ.DataSet

getLabelFields() - Method in class org.molgenis.omx.observ.ObservableFeature

getLabelFields() - Method in class org.molgenis.omx.observ.ObservationSet

getLabelFields() - Method in class org.molgenis.omx.observ.ObservationTarget

getLabelFields() - Method in class org.molgenis.omx.observ.ObservedValue

getLabelFields() - Method in class org.molgenis.omx.observ.Protocol

getLabelFields() - Method in class org.molgenis.omx.observ.Protocol_Features

getLabelFields() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getLabelFields() - Method in class org.molgenis.omx.observ.target.Accession

getLabelFields() - Method in class org.molgenis.omx.observ.target.Individual

getLabelFields() - Method in class org.molgenis.omx.observ.target.Ontology

getLabelFields() - Method in class org.molgenis.omx.observ.target.OntologyTerm

getLabelFields() - Method in class org.molgenis.omx.observ.target.Panel

getLabelFields() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getLabelFields() - Method in class org.molgenis.omx.observ.target.PanelSource

getLabelFields() - Method in class org.molgenis.omx.observ.target.Species

getLabelFields() - Method in class org.molgenis.omx.observ.value.BoolValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.CategoricalValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.DateTimeValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.DateValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.DecimalValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.EmailValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.HtmlValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.HyperlinkValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.IntValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.LongValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.MrefValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

getLabelFields() - Method in class org.molgenis.omx.observ.value.StringValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.TextValue

getLabelFields() - Method in class org.molgenis.omx.observ.value.Value

getLabelFields() - Method in class org.molgenis.omx.observ.value.XrefValue

getMother() - Method in class org.molgenis.omx.observ.target.Individual

Get the Refers to the mother of the individual..

getMother(Database) - Method in class org.molgenis.omx.observ.target.Individual

Deprecated.

getMother_Id() - Method in class org.molgenis.omx.observ.target.Individual

getMother_Identifier() - Method in class org.molgenis.omx.observ.target.Individual

Get a pretty label Identifier for cross reference Mother to Individual.Id.

getMrefValue() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Get the .

getMrefValue(Database) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Deprecated.

getMrefValue_Id() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

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(Database) - Method in class org.molgenis.omx.core.MolgenisEntity

Deprecated.

getName() - Method in class org.molgenis.omx.core.MolgenisFile

Get the human readible name, not necessary unique..

getName(Database) - Method in class org.molgenis.omx.core.MolgenisFile

Deprecated.

getName() - Method in class org.molgenis.omx.core.RuntimeProperty

Get the human readible name, not necessary unique..

getName(Database) - Method in class org.molgenis.omx.core.RuntimeProperty

Deprecated.

getName() - Method in class org.molgenis.omx.observ.Characteristic

Get the human readible name, not necessary unique..

getName(Database) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

getName() - Method in class org.molgenis.omx.observ.target.Ontology

Get the human readible name, not necessary unique..

getName(Database) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getNeededExtraFields(String, Database) - Static method in class org.molgenis.omx.services.FileUploadUtils

Reusable function that will return a list of fieldnames that are needed for this subclass of 'MolgenisFile'.

getNumberOfIndividuals() - Method in class org.molgenis.omx.observ.target.Panel

Get the NumberOfIndividuals.

getNumberOfIndividuals(Database) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getNumberOfIndividuals() - Method in class org.molgenis.omx.observ.target.PanelSource

Get the Number of individuals lifted over from this source.

getNumberOfIndividuals(Database) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getObservableFeature() - Method in class org.molgenis.omx.observ.Category

Get the The Measurement these permitted values are part of..

getObservableFeature(Database) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getObservableFeature_Id() - Method in class org.molgenis.omx.observ.Category

getObservableFeature_Identifier() - Method in class org.molgenis.omx.observ.Category

Get a pretty label Identifier for cross reference ObservableFeature to ObservableFeature.Id.

getObservationSet() - Method in class org.molgenis.omx.observ.ObservedValue

Get the Reference to the observation.

getObservationSet(Database) - Method in class org.molgenis.omx.observ.ObservedValue

Deprecated.

getObservationSet_Id() - Method in class org.molgenis.omx.observ.ObservedValue

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..

getOntology(Database) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Deprecated.

getOntology_Id() - Method in class org.molgenis.omx.observ.target.OntologyTerm

getOntology_Identifier() - Method in class org.molgenis.omx.observ.target.OntologyTerm

Get a pretty label Identifier for cross reference Ontology to Ontology.Id.

getOntologyAccession() - Method in class org.molgenis.omx.observ.target.Ontology

Get the A accession that uniquely identifies the ontology (typically an acronym).

getOntologyAccession(Database) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getOntologyURI() - Method in class org.molgenis.omx.observ.target.Ontology

Get the (Optional) A URI that references the location of the ontology..

getOntologyURI(Database) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getPanel() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Get the .

getPanel(Database) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Deprecated.

getPanel_Id() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getPanel_Identifier() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Get a pretty label Identifier for cross reference Panel to Panel.Id.

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).

getPanelType(Database) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getPanelType_Id() - Method in class org.molgenis.omx.observ.target.Panel

getPanelType_Identifier() - Method in class org.molgenis.omx.observ.target.Panel

Get a pretty label Identifier for cross reference PanelType to OntologyTerm.Id.

getPartOfDataSet() - Method in class org.molgenis.omx.observ.ObservationSet

Get the DataSet this ValueSet is part of..

getPartOfDataSet(Database) - Method in class org.molgenis.omx.observ.ObservationSet

Deprecated.

getPartOfDataSet_Id() - Method in class org.molgenis.omx.observ.ObservationSet

getPartOfDataSet_Identifier() - Method in class org.molgenis.omx.observ.ObservationSet

Get a pretty label Identifier for cross reference PartOfDataSet to DataSet.Id.

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(Database) - Method in class org.molgenis.omx.observ.Protocol_Features

Deprecated.

getProtocol() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Get the .

getProtocol(Database) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Deprecated.

getProtocol_Id() - Method in class org.molgenis.omx.observ.Protocol_Features

getProtocol_Id() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getProtocol_Identifier() - Method in class org.molgenis.omx.observ.Protocol_Features

Get a pretty label Identifier for cross reference Protocol to Protocol.Id.

getProtocol_Identifier() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Get a pretty label Identifier for cross reference Protocol to Protocol.Id.

getProtocolDescendants(Protocol) - Static method in class org.molgenis.omx.utils.ProtocolUtils

Returns the descendants of the given protocol including the given protocol

getProtocolType() - Method in class org.molgenis.omx.observ.Protocol

Get the classification of protocol.

getProtocolType(Database) - Method in class org.molgenis.omx.observ.Protocol

Deprecated.

getProtocolType_Id() - Method in class org.molgenis.omx.observ.Protocol

getProtocolType_Identifier() - Method in class org.molgenis.omx.observ.Protocol

Get a pretty label Identifier for cross reference ProtocolType to OntologyTerm.Id.

getProtocolUsed() - Method in class org.molgenis.omx.observ.DataSet

Get the Reference to the protocol that is being used (if available).

getProtocolUsed(Database) - Method in class org.molgenis.omx.observ.DataSet

Deprecated.

getProtocolUsed_Id() - Method in class org.molgenis.omx.observ.DataSet

getProtocolUsed_Identifier() - Method in class org.molgenis.omx.observ.DataSet

Get a pretty label Identifier for cross reference ProtocolUsed to Protocol.Id.

getReport() - Method in class org.molgenis.omx.services.StorageHandler

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.

getSelectionCriteria(Database) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getSourcePanel() - Method in class org.molgenis.omx.observ.target.PanelSource

Get the Source that contributed individuals to current panel.

getSourcePanel(Database) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getSourcePanel_Id() - Method in class org.molgenis.omx.observ.target.PanelSource

getSourcePanel_Identifier() - Method in class org.molgenis.omx.observ.target.PanelSource

Get a pretty label Identifier for cross reference SourcePanel to Panel.Id.

getSpecies() - Method in class org.molgenis.omx.observ.target.Panel

Get the The species this panel is an instance of/part of/extracted from..

getSpecies(Database) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getSpecies_Id() - Method in class org.molgenis.omx.observ.target.Panel

getSpecies_Identifier() - Method in class org.molgenis.omx.observ.target.Panel

Get a pretty label Identifier for cross reference Species to Species.Id.

getStartTime() - Method in class org.molgenis.omx.observ.DataSet

Get the time when the protocol started..

getStartTime(Database) - Method in class org.molgenis.omx.observ.DataSet

Deprecated.

getStorageDirFor(MolgenisFile, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Get the storage directory for this MolgenisFile object.

getStorageDirFor(String, Database) - Method in class org.molgenis.omx.decorators.MolgenisFileHandler

Get the storage directory for a type of file denoted by this String.

getSubprotocols() - Method in class org.molgenis.omx.observ.Protocol

Get the Subprotocols of this protocol.

getSubprotocols(Database) - Method in class org.molgenis.omx.observ.Protocol

Deprecated.

getSubprotocols() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Get the .

getSubprotocols(Database) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Deprecated.

getSubprotocols_Id() - Method in class org.molgenis.omx.observ.Protocol

getSubprotocols_Id() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getSubprotocols_Identifier() - Method in class org.molgenis.omx.observ.Protocol

Get a pretty label for cross reference Subprotocols to Protocol.Id.

getSubprotocols_Identifier() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Get a pretty label Identifier for cross reference Subprotocols to Protocol.Id.

getSubprotocolsProtocolCollection() - Method in class org.molgenis.omx.observ.Protocol

getSubprotocolsProtocolCollection(Database) - Method in class org.molgenis.omx.observ.Protocol

getTableFieldName(String) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

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.

getTemporal(Database) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

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.

getTermAccession(Database) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Deprecated.

getTime() - Method in class org.molgenis.omx.observ.ObservationSet

Get the Time of this observationSet.

getTime(Database) - Method in class org.molgenis.omx.observ.ObservationSet

Deprecated.

getType() - Method in class org.molgenis.omx.core.MolgenisEntity

Get the Type of the entity.

getType(Database) - Method in class org.molgenis.omx.core.MolgenisEntity

Deprecated.

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).

getUnit(Database) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

getUnit_Id() - Method in class org.molgenis.omx.observ.ObservableFeature

getUnit_Identifier() - Method in class org.molgenis.omx.observ.ObservableFeature

Get a pretty label Identifier for cross reference Unit to OntologyTerm.Id.

getValue() - Method in class org.molgenis.omx.core.RuntimeProperty

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.core.RuntimeProperty

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.ObservedValue

Get the The value observed.

getValue(Database) - Method in class org.molgenis.omx.observ.ObservedValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.BoolValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.BoolValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.CategoricalValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.DateTimeValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.DateTimeValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.DateValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.DateValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.DecimalValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.DecimalValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.EmailValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.EmailValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.HtmlValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.HtmlValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.IntValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.IntValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.LongValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.LongValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.MrefValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.MrefValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Get the .

getValue(Database) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.StringValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.StringValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.TextValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.TextValue

Deprecated.

getValue() - Method in class org.molgenis.omx.observ.value.XrefValue

Get the Value.

getValue(Database) - Method in class org.molgenis.omx.observ.value.XrefValue

Deprecated.

getValue() - Method in class org.molgenis.omx.utils.ValueCell

getValue_Id() - Method in class org.molgenis.omx.observ.ObservedValue

getValue_Id() - Method in class org.molgenis.omx.observ.value.CategoricalValue

getValue_Id() - Method in class org.molgenis.omx.observ.value.MrefValue

getValue_Id() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

getValue_Id() - Method in class org.molgenis.omx.observ.value.XrefValue

getValue_Identifier() - Method in class org.molgenis.omx.observ.value.CategoricalValue

Get a pretty label Identifier for cross reference Value to Category.Id.

getValue_Identifier() - Method in class org.molgenis.omx.observ.value.MrefValue

Get a pretty label for cross reference Value to Characteristic.Id.

getValue_Identifier() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Get a pretty label Identifier for cross reference Value to Characteristic.Id.

getValue_Identifier() - Method in class org.molgenis.omx.observ.value.XrefValue

Get a pretty label Identifier for cross reference Value to Characteristic.Id.

getValueCode() - Method in class org.molgenis.omx.observ.Category

Get the The value used to store this category in ObservedValue.

getValueCode(Database) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getValueMrefValueCollection() - Method in class org.molgenis.omx.observ.Characteristic

getValueMrefValueCollection(Database) - Method in class org.molgenis.omx.observ.Characteristic

getValues(String) - Method in class org.molgenis.omx.core.MolgenisEntity

Deprecated.

getValues(String) - Method in class org.molgenis.omx.core.MolgenisFile

Deprecated.

getValues(String) - Method in class org.molgenis.omx.core.RuntimeProperty

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.Category

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.Characteristic

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.DataSet

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.ObservableFeature

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.ObservationSet

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.ObservationTarget

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.ObservedValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.Protocol

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.Protocol_Features

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Accession

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Individual

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Ontology

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Panel

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.PanelSource

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.target.Species

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.BoolValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.DateTimeValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.DateValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.DecimalValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.EmailValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.HtmlValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.IntValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.LongValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.MrefValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.StringValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.TextValue

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.Value

Deprecated.

getValues(String) - Method in class org.molgenis.omx.observ.value.XrefValue

Deprecated.

getVerified() - Method in class org.molgenis.omx.services.Report

getXrefIdFieldName(String) - Method in class org.molgenis.omx.core.MolgenisEntity

getXrefIdFieldName(String) - Method in class org.molgenis.omx.core.MolgenisFile

getXrefIdFieldName(String) - Method in class org.molgenis.omx.core.RuntimeProperty

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.Category

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.Characteristic

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.DataSet

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.ObservableFeature

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.ObservationSet

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.ObservationTarget

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.ObservedValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.Protocol

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.Protocol_Features

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Accession

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Individual

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Ontology

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Panel

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.PanelSource

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.target.Species

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.BoolValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.CategoricalValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.DateTimeValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.DateValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.DecimalValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.EmailValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.HtmlValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.IntValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.LongValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.MrefValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.StringValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.TextValue

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.Value

getXrefIdFieldName(String) - Method in class org.molgenis.omx.observ.value.XrefValue

H

handleRequest(MolgenisRequest, MolgenisResponse) - Method in class org.molgenis.omx.services.FileDownloadService

handleRequest(MolgenisRequest, MolgenisResponse) - Method in class org.molgenis.omx.services.FileUploadService

handleRequest(MolgenisRequest, MolgenisResponse) - Method in class org.molgenis.omx.services.FileViewService

hasFileStorage(boolean, Database) - 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.core.MolgenisEntity

hashCode() - Method in class org.molgenis.omx.core.MolgenisFile

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.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_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.utils.ValueCell

hasNext() - Method in class org.molgenis.omx.dataset.DataSetTableIterator

hasValidFileStorage(Database) - 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

HtmlValue(HtmlValue) - Constructor for class org.molgenis.omx.observ.value.HtmlValue

copy constructor

HtmlValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads HtmlValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

HtmlValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.HtmlValueEntityImporter

HtmlValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity HtmlValue

HtmlValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.HtmlValueForm

HtmlValueForm(HtmlValue) - Constructor for class org.molgenis.omx.observ.value.ui.HtmlValueForm

HtmlValueJpaMapper - Class in org.molgenis.omx.observ.value.db

HtmlValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

HtmlValueService - Class in org.molgenis.service

HtmlValueService() - Constructor for class org.molgenis.service.HtmlValueService

HyperlinkValue - Class in org.molgenis.omx.observ.value

HyperlinkValue: .

HyperlinkValue() - Constructor for class org.molgenis.omx.observ.value.HyperlinkValue

HyperlinkValue(HyperlinkValue) - Constructor for class org.molgenis.omx.observ.value.HyperlinkValue

copy constructor

HyperlinkValueDecorator<E extends HyperlinkValue> - Class in org.molgenis.omx.decorators

HyperlinkValueDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.decorators.HyperlinkValueDecorator

HyperlinkValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads HyperlinkValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

HyperlinkValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.HyperlinkValueEntityImporter

HyperlinkValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity HyperlinkValue

HyperlinkValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.HyperlinkValueForm

HyperlinkValueForm(HyperlinkValue) - Constructor for class org.molgenis.omx.observ.value.ui.HyperlinkValueForm

HyperlinkValueJpaMapper - Class in org.molgenis.omx.observ.value.db

HyperlinkValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

HyperlinkValueService - Class in org.molgenis.service

HyperlinkValueService() - Constructor for class org.molgenis.service.HyperlinkValueService

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.core.MolgenisEntity

ID - Static variable in class org.molgenis.omx.core.MolgenisFile

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.MolgenisFile

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.target.Ontology

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.core.db.MolgenisEntityEntityImporter

Imports MolgenisEntity from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.core.db.MolgenisFileEntityImporter

Imports MolgenisFile from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.core.db.RuntimePropertyEntityImporter

Imports RuntimeProperty from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.CategoryEntityImporter

Imports Category from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.CharacteristicEntityImporter

Imports Characteristic from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.DataSetEntityImporter

Imports DataSet from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.ObservableFeatureEntityImporter

Imports ObservableFeature from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.ObservationSetEntityImporter

Imports ObservationSet from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.ObservationTargetEntityImporter

Imports ObservationTarget from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.ObservedValueEntityImporter

Imports ObservedValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesEntityImporter

Imports Protocol_Features from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsEntityImporter

Imports Protocol_Subprotocols from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.db.ProtocolEntityImporter

Imports Protocol from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.AccessionEntityImporter

Imports Accession from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.IndividualEntityImporter

Imports Individual from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.OntologyEntityImporter

Imports Ontology from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.OntologyTermEntityImporter

Imports OntologyTerm from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsEntityImporter

Imports Panel_Individuals from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.PanelEntityImporter

Imports Panel from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.PanelSourceEntityImporter

Imports PanelSource from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.target.db.SpeciesEntityImporter

Imports Species from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.BoolValueEntityImporter

Imports BoolValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueEntityImporter

Imports CategoricalValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueEntityImporter

Imports DateTimeValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.DateValueEntityImporter

Imports DateValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.DecimalValueEntityImporter

Imports DecimalValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.EmailValueEntityImporter

Imports EmailValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.HtmlValueEntityImporter

Imports HtmlValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueEntityImporter

Imports HyperlinkValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.IntValueEntityImporter

Imports IntValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.LongValueEntityImporter

Imports LongValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueEntityImporter

Imports MrefValue_Value from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.MrefValueEntityImporter

Imports MrefValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.StringValueEntityImporter

Imports StringValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.TextValueEntityImporter

Imports TextValue from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.ValueEntityImporter

Imports Value from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.observ.value.db.XrefValueEntityImporter

Imports XrefValue from tab/comma delimited File

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

Individual(Individual) - Constructor for class org.molgenis.omx.observ.target.Individual

copy constructor

IndividualEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Individual from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

IndividualEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.IndividualEntityImporter

IndividualForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Individual

IndividualForm() - Constructor for class org.molgenis.omx.observ.target.ui.IndividualForm

IndividualForm(Individual) - Constructor for class org.molgenis.omx.observ.target.ui.IndividualForm

IndividualJpaMapper - Class in org.molgenis.omx.observ.target.db

IndividualJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.IndividualJpaMapper

INDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.Panel

INDIVIDUALS - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals

INDIVIDUALS_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Panel

INDIVIDUALS_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals

IndividualService - Class in org.molgenis.service

IndividualService() - Constructor for class org.molgenis.service.IndividualService

IntValue - Class in org.molgenis.omx.observ.value

IntValue: .

IntValue() - Constructor for class org.molgenis.omx.observ.value.IntValue

IntValue(IntValue) - Constructor for class org.molgenis.omx.observ.value.IntValue

copy constructor

IntValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads IntValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

IntValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.IntValueEntityImporter

IntValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity IntValue

IntValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.IntValueForm

IntValueForm(IntValue) - Constructor for class org.molgenis.omx.observ.value.ui.IntValueForm

IntValueJpaMapper - Class in org.molgenis.omx.observ.value.db

IntValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.IntValueJpaMapper

IntValueService - Class in org.molgenis.service

IntValueService() - Constructor for class org.molgenis.service.IntValueService

ISMISSING - Static variable in class org.molgenis.omx.observ.Category

iterator() - Method in class org.molgenis.omx.dataset.DataSetTable

iterator() - Method in class org.molgenis.omx.protocol.ProtocolTable

L

LongValue - Class in org.molgenis.omx.observ.value

LongValue: .

LongValue() - Constructor for class org.molgenis.omx.observ.value.LongValue

LongValue(LongValue) - Constructor for class org.molgenis.omx.observ.value.LongValue

copy constructor

LongValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads LongValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

LongValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.LongValueEntityImporter

LongValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity LongValue

LongValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.LongValueForm

LongValueForm(LongValue) - Constructor for class org.molgenis.omx.observ.value.ui.LongValueForm

LongValueJpaMapper - Class in org.molgenis.omx.observ.value.db

LongValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.LongValueJpaMapper

LongValueService - Class in org.molgenis.service

LongValueService() - Constructor for class org.molgenis.service.LongValueService

M

MolgenisDbSettings - Class in org.molgenis.omx

MolgenisDbSettings() - 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

MolgenisEntity(MolgenisEntity) - Constructor for class org.molgenis.omx.core.MolgenisEntity

copy constructor

MolgenisEntityEntityImporter - Class in org.molgenis.omx.core.db

Reads MolgenisEntity from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MolgenisEntityEntityImporter() - Constructor for class org.molgenis.omx.core.db.MolgenisEntityEntityImporter

MolgenisEntityForm - Class in org.molgenis.omx.core.ui

A HtmlForm that is preloaded with all inputs for entity MolgenisEntity

MolgenisEntityForm() - Constructor for class org.molgenis.omx.core.ui.MolgenisEntityForm

MolgenisEntityForm(MolgenisEntity) - Constructor for class org.molgenis.omx.core.ui.MolgenisEntityForm

MolgenisEntityJpaMapper - Class in org.molgenis.omx.core.db

MolgenisEntityJpaMapper(Database) - Constructor for class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

MolgenisFile - Class in org.molgenis.omx.core

MolgenisFile: Helper entity to deal with files.

MolgenisFile() - Constructor for class org.molgenis.omx.core.MolgenisFile

MolgenisFile(MolgenisFile) - Constructor for class org.molgenis.omx.core.MolgenisFile

copy constructor

MolgenisFileDecorator<E extends MolgenisFile> - Class in org.molgenis.omx.decorators

Generic decorator for MOLGENIS files.

MolgenisFileDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.decorators.MolgenisFileDecorator

MolgenisFileEntityImporter - Class in org.molgenis.omx.core.db

Reads MolgenisFile from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MolgenisFileEntityImporter() - Constructor for class org.molgenis.omx.core.db.MolgenisFileEntityImporter

MolgenisFileForm - Class in org.molgenis.omx.core.ui

A HtmlForm that is preloaded with all inputs for entity MolgenisFile

MolgenisFileForm() - Constructor for class org.molgenis.omx.core.ui.MolgenisFileForm

MolgenisFileForm(MolgenisFile) - Constructor for class org.molgenis.omx.core.ui.MolgenisFileForm

MolgenisFileHandler - Class in org.molgenis.omx.decorators

MolgenisFileHandler(Database) - Constructor for class org.molgenis.omx.decorators.MolgenisFileHandler

MolgenisFileHandler.TypeUnknownException - Exception in org.molgenis.omx.decorators

MolgenisFileHandler.TypeUnknownException(String) - Constructor for exception org.molgenis.omx.decorators.MolgenisFileHandler.TypeUnknownException

MolgenisFileJpaMapper - Class in org.molgenis.omx.core.db

MolgenisFileJpaMapper(Database) - Constructor for class org.molgenis.omx.core.db.MolgenisFileJpaMapper

MolgenisFileService - Class in org.molgenis.service

MolgenisFileService() - Constructor for class org.molgenis.service.MolgenisFileService

molgenisSettings() - Method in class org.molgenis.omx.OmxConfig

MOTHER - Static variable in class org.molgenis.omx.observ.target.Individual

MOTHER_IDENTIFIER - 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(MrefValue) - Constructor for class org.molgenis.omx.observ.value.MrefValue

copy constructor

MREFVALUE - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value

MREFVALUE_ID - 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_Value(MrefValue_Value) - Constructor for class org.molgenis.omx.observ.value.MrefValue_Value

copy constructor

MrefValue_ValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads MrefValue_Value from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MrefValue_ValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.MrefValue_ValueEntityImporter

MrefValue_ValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity MrefValue_Value

MrefValue_ValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.MrefValue_ValueForm

MrefValue_ValueForm(MrefValue_Value) - Constructor for class org.molgenis.omx.observ.value.ui.MrefValue_ValueForm

MrefValue_ValueJpaMapper - Class in org.molgenis.omx.observ.value.db

MrefValue_ValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

MrefValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads MrefValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MrefValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.MrefValueEntityImporter

MrefValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity MrefValue

MrefValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.MrefValueForm

MrefValueForm(MrefValue) - Constructor for class org.molgenis.omx.observ.value.ui.MrefValueForm

MrefValueJpaMapper - Class in org.molgenis.omx.observ.value.db

MrefValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

MrefValueService - Class in org.molgenis.service

MrefValueService() - Constructor for class org.molgenis.service.MrefValueService

N

NAME - Static variable in class org.molgenis.omx.core.MolgenisEntity

NAME - Static variable in class org.molgenis.omx.core.MolgenisFile

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

next() - Method in class org.molgenis.omx.dataset.DataSetTableIterator

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(ObservableFeature) - Constructor for class org.molgenis.omx.observ.ObservableFeature

copy constructor

OBSERVABLEFEATURE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Category

ObservableFeatureEntityImporter - Class in org.molgenis.omx.observ.db

Reads ObservableFeature from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ObservableFeatureEntityImporter() - Constructor for class org.molgenis.omx.observ.db.ObservableFeatureEntityImporter

ObservableFeatureForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity ObservableFeature

ObservableFeatureForm() - Constructor for class org.molgenis.omx.observ.ui.ObservableFeatureForm

ObservableFeatureForm(ObservableFeature) - Constructor for class org.molgenis.omx.observ.ui.ObservableFeatureForm

ObservableFeatureJpaMapper - Class in org.molgenis.omx.observ.db

ObservableFeatureJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

ObservableFeatureService - Class in org.molgenis.service

ObservableFeatureService() - Constructor for class org.molgenis.service.ObservableFeatureService

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(ObservationSet) - Constructor for class org.molgenis.omx.observ.ObservationSet

copy constructor

OBSERVATIONSET - Static variable in class org.molgenis.omx.observ.ObservedValue

OBSERVATIONSET_ID - Static variable in class org.molgenis.omx.observ.ObservedValue

ObservationSetEntityImporter - Class in org.molgenis.omx.observ.db

Reads ObservationSet from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ObservationSetEntityImporter() - Constructor for class org.molgenis.omx.observ.db.ObservationSetEntityImporter

ObservationSetForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity ObservationSet

ObservationSetForm() - Constructor for class org.molgenis.omx.observ.ui.ObservationSetForm

ObservationSetForm(ObservationSet) - Constructor for class org.molgenis.omx.observ.ui.ObservationSetForm

ObservationSetJpaMapper - Class in org.molgenis.omx.observ.db

ObservationSetJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.ObservationSetJpaMapper

ObservationSetService - Class in org.molgenis.service

ObservationSetService() - Constructor for class org.molgenis.service.ObservationSetService

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

ObservationTarget(ObservationTarget) - Constructor for class org.molgenis.omx.observ.ObservationTarget

copy constructor

ObservationTargetEntityImporter - Class in org.molgenis.omx.observ.db

Reads ObservationTarget from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ObservationTargetEntityImporter() - Constructor for class org.molgenis.omx.observ.db.ObservationTargetEntityImporter

ObservationTargetForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity ObservationTarget

ObservationTargetForm() - Constructor for class org.molgenis.omx.observ.ui.ObservationTargetForm

ObservationTargetForm(ObservationTarget) - Constructor for class org.molgenis.omx.observ.ui.ObservationTargetForm

ObservationTargetJpaMapper - Class in org.molgenis.omx.observ.db

ObservationTargetJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

ObservationTargetService - Class in org.molgenis.service

ObservationTargetService() - Constructor for class org.molgenis.service.ObservationTargetService

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

ObservedValue(ObservedValue) - Constructor for class org.molgenis.omx.observ.ObservedValue

copy constructor

ObservedValueEntityImporter - Class in org.molgenis.omx.observ.db

Reads ObservedValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ObservedValueEntityImporter() - Constructor for class org.molgenis.omx.observ.db.ObservedValueEntityImporter

ObservedValueForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity ObservedValue

ObservedValueForm() - Constructor for class org.molgenis.omx.observ.ui.ObservedValueForm

ObservedValueForm(ObservedValue) - Constructor for class org.molgenis.omx.observ.ui.ObservedValueForm

ObservedValueJpaMapper - Class in org.molgenis.omx.observ.db

ObservedValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.ObservedValueJpaMapper

ObservedValueService - Class in org.molgenis.service

ObservedValueService() - Constructor for class org.molgenis.service.ObservedValueService

OmxConfig - Class in org.molgenis.omx

OmxConfig() - Constructor for class org.molgenis.omx.OmxConfig

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(Ontology) - Constructor for class org.molgenis.omx.observ.target.Ontology

copy constructor

ONTOLOGY - Static variable in class org.molgenis.omx.observ.target.OntologyTerm

ONTOLOGY_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.OntologyTerm

ONTOLOGYACCESSION - Static variable in class org.molgenis.omx.observ.target.Ontology

OntologyEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Ontology from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

OntologyEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.OntologyEntityImporter

OntologyForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Ontology

OntologyForm() - Constructor for class org.molgenis.omx.observ.target.ui.OntologyForm

OntologyForm(Ontology) - Constructor for class org.molgenis.omx.observ.target.ui.OntologyForm

OntologyJpaMapper - Class in org.molgenis.omx.observ.target.db

OntologyJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.OntologyJpaMapper

OntologyService - Class in org.molgenis.service

OntologyService() - Constructor for class org.molgenis.service.OntologyService

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

OntologyTerm(OntologyTerm) - Constructor for class org.molgenis.omx.observ.target.OntologyTerm

copy constructor

OntologyTermEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads OntologyTerm from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

OntologyTermEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.OntologyTermEntityImporter

OntologyTermForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity OntologyTerm

OntologyTermForm() - Constructor for class org.molgenis.omx.observ.target.ui.OntologyTermForm

OntologyTermForm(OntologyTerm) - Constructor for class org.molgenis.omx.observ.target.ui.OntologyTermForm

OntologyTermJpaMapper - Class in org.molgenis.omx.observ.target.db

OntologyTermJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

OntologyTermService - Class in org.molgenis.service

OntologyTermService() - Constructor for class org.molgenis.service.OntologyTermService

ONTOLOGYURI - Static variable in class org.molgenis.omx.observ.target.Ontology

org.molgenis.omx - package org.molgenis.omx

org.molgenis.omx.cart - package org.molgenis.omx.cart

org.molgenis.omx.converters - package org.molgenis.omx.converters

org.molgenis.omx.core - package org.molgenis.omx.core

org.molgenis.omx.core.db - package org.molgenis.omx.core.db

org.molgenis.omx.core.ui - package org.molgenis.omx.core.ui

org.molgenis.omx.dataset - package org.molgenis.omx.dataset

org.molgenis.omx.decorators - package org.molgenis.omx.decorators

org.molgenis.omx.observ - package org.molgenis.omx.observ

org.molgenis.omx.observ.db - package org.molgenis.omx.observ.db

org.molgenis.omx.observ.target - package org.molgenis.omx.observ.target

org.molgenis.omx.observ.target.db - package org.molgenis.omx.observ.target.db

org.molgenis.omx.observ.target.ui - package org.molgenis.omx.observ.target.ui

org.molgenis.omx.observ.ui - package org.molgenis.omx.observ.ui

org.molgenis.omx.observ.value - package org.molgenis.omx.observ.value

org.molgenis.omx.observ.value.db - package org.molgenis.omx.observ.value.db

org.molgenis.omx.observ.value.ui - package org.molgenis.omx.observ.value.ui

org.molgenis.omx.protocol - package org.molgenis.omx.protocol

org.molgenis.omx.services - package org.molgenis.omx.services

org.molgenis.omx.utils - package org.molgenis.omx.utils

org.molgenis.service - package org.molgenis.service

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(Panel) - Constructor for class org.molgenis.omx.observ.target.Panel

copy constructor

PANEL - Static variable in class org.molgenis.omx.observ.target.Panel_Individuals

PANEL_IDENTIFIER - 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_Individuals(Panel_Individuals) - Constructor for class org.molgenis.omx.observ.target.Panel_Individuals

copy constructor

Panel_IndividualsEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Panel_Individuals from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

Panel_IndividualsEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.Panel_IndividualsEntityImporter

Panel_IndividualsForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Panel_Individuals

Panel_IndividualsForm() - Constructor for class org.molgenis.omx.observ.target.ui.Panel_IndividualsForm

Panel_IndividualsForm(Panel_Individuals) - Constructor for class org.molgenis.omx.observ.target.ui.Panel_IndividualsForm

Panel_IndividualsJpaMapper - Class in org.molgenis.omx.observ.target.db

Panel_IndividualsJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

PanelEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Panel from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

PanelEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.PanelEntityImporter

PanelForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Panel

PanelForm() - Constructor for class org.molgenis.omx.observ.target.ui.PanelForm

PanelForm(Panel) - Constructor for class org.molgenis.omx.observ.target.ui.PanelForm

PanelJpaMapper - Class in org.molgenis.omx.observ.target.db

PanelJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.PanelJpaMapper

PanelService - Class in org.molgenis.service

PanelService() - Constructor for class org.molgenis.service.PanelService

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

PanelSource(PanelSource) - Constructor for class org.molgenis.omx.observ.target.PanelSource

copy constructor

PanelSourceEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads PanelSource from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

PanelSourceEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.PanelSourceEntityImporter

PanelSourceForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity PanelSource

PanelSourceForm() - Constructor for class org.molgenis.omx.observ.target.ui.PanelSourceForm

PanelSourceForm(PanelSource) - Constructor for class org.molgenis.omx.observ.target.ui.PanelSourceForm

PanelSourceJpaMapper - Class in org.molgenis.omx.observ.target.db

PanelSourceJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

PanelSourceService - Class in org.molgenis.service

PanelSourceService() - Constructor for class org.molgenis.service.PanelSourceService

PANELTYPE - Static variable in class org.molgenis.omx.observ.target.Panel

PANELTYPE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Panel

PARTOFDATASET - Static variable in class org.molgenis.omx.observ.ObservationSet

PARTOFDATASET_IDENTIFIER - Static variable in class org.molgenis.omx.observ.ObservationSet

prepareFileAttachements(List<MolgenisEntity>, File) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

prepareFileAttachements(List<MolgenisFile>, File) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

prepareFileAttachements(List<RuntimeProperty>, File) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

prepareFileAttachements(List<Category>, File) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

prepareFileAttachements(List<Characteristic>, File) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

prepareFileAttachements(List<DataSet>, File) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

prepareFileAttachements(List<ObservableFeature>, File) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

prepareFileAttachements(List<ObservationSet>, File) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

prepareFileAttachements(List<ObservationTarget>, File) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

prepareFileAttachements(List<ObservedValue>, File) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

prepareFileAttachements(List<Protocol_Features>, File) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

prepareFileAttachements(List<Protocol_Subprotocols>, File) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

prepareFileAttachements(List<Protocol>, File) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

prepareFileAttachements(List<Accession>, File) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

prepareFileAttachements(List<Individual>, File) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

prepareFileAttachements(List<Ontology>, File) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

prepareFileAttachements(List<OntologyTerm>, File) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

prepareFileAttachements(List<Panel_Individuals>, File) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

prepareFileAttachements(List<Panel>, File) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

prepareFileAttachements(List<PanelSource>, File) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

prepareFileAttachements(List<Species>, File) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

prepareFileAttachements(List<BoolValue>, File) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

prepareFileAttachements(List<CategoricalValue>, File) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

prepareFileAttachements(List<DateTimeValue>, File) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

prepareFileAttachements(List<DateValue>, File) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

prepareFileAttachements(List<DecimalValue>, File) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

prepareFileAttachements(List<EmailValue>, File) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

prepareFileAttachements(List<HtmlValue>, File) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

prepareFileAttachements(List<HyperlinkValue>, File) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

prepareFileAttachements(List<IntValue>, File) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

prepareFileAttachements(List<LongValue>, File) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

prepareFileAttachements(List<MrefValue_Value>, File) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

prepareFileAttachements(List<MrefValue>, File) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

prepareFileAttachements(List<StringValue>, File) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

prepareFileAttachements(List<TextValue>, File) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

prepareFileAttachements(List<Value>, File) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

prepareFileAttachements(List<XrefValue>, File) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

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(Protocol) - Constructor for class org.molgenis.omx.observ.Protocol

copy constructor

PROTOCOL - Static variable in class org.molgenis.omx.observ.Protocol_Features

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_Features(Protocol_Features) - Constructor for class org.molgenis.omx.observ.Protocol_Features

copy constructor

Protocol_FeaturesEntityImporter - Class in org.molgenis.omx.observ.db

Reads Protocol_Features from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

Protocol_FeaturesEntityImporter() - Constructor for class org.molgenis.omx.observ.db.Protocol_FeaturesEntityImporter

Protocol_FeaturesForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity Protocol_Features

Protocol_FeaturesForm() - Constructor for class org.molgenis.omx.observ.ui.Protocol_FeaturesForm

Protocol_FeaturesForm(Protocol_Features) - Constructor for class org.molgenis.omx.observ.ui.Protocol_FeaturesForm

Protocol_FeaturesJpaMapper - Class in org.molgenis.omx.observ.db

Protocol_FeaturesJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

PROTOCOL_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol_Features

PROTOCOL_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols

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_Subprotocols(Protocol_Subprotocols) - Constructor for class org.molgenis.omx.observ.Protocol_Subprotocols

copy constructor

Protocol_SubprotocolsEntityImporter - Class in org.molgenis.omx.observ.db

Reads Protocol_Subprotocols from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

Protocol_SubprotocolsEntityImporter() - Constructor for class org.molgenis.omx.observ.db.Protocol_SubprotocolsEntityImporter

Protocol_SubprotocolsForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity Protocol_Subprotocols

Protocol_SubprotocolsForm() - Constructor for class org.molgenis.omx.observ.ui.Protocol_SubprotocolsForm

Protocol_SubprotocolsForm(Protocol_Subprotocols) - Constructor for class org.molgenis.omx.observ.ui.Protocol_SubprotocolsForm

Protocol_SubprotocolsJpaMapper - Class in org.molgenis.omx.observ.db

Protocol_SubprotocolsJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

ProtocolEntityImporter - Class in org.molgenis.omx.observ.db

Reads Protocol from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ProtocolEntityImporter() - Constructor for class org.molgenis.omx.observ.db.ProtocolEntityImporter

ProtocolForm - Class in org.molgenis.omx.observ.ui

A HtmlForm that is preloaded with all inputs for entity Protocol

ProtocolForm() - Constructor for class org.molgenis.omx.observ.ui.ProtocolForm

ProtocolForm(Protocol) - Constructor for class org.molgenis.omx.observ.ui.ProtocolForm

ProtocolJpaMapper - Class in org.molgenis.omx.observ.db

ProtocolJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.db.ProtocolJpaMapper

ProtocolService - Class in org.molgenis.service

ProtocolService() - Constructor for class org.molgenis.service.ProtocolService

ProtocolTable - Class in org.molgenis.omx.protocol

ProtocolTable(Protocol, Database) - Constructor for class org.molgenis.omx.protocol.ProtocolTable

PROTOCOLTYPE - Static variable in class org.molgenis.omx.observ.Protocol

PROTOCOLTYPE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol

PROTOCOLUSED - Static variable in class org.molgenis.omx.observ.DataSet

PROTOCOLUSED_IDENTIFIER - 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(Database) - Static method in class org.molgenis.omx.core.MolgenisEntity

Shorthand for db.query(MolgenisEntity.class).

query(Database) - Static method in class org.molgenis.omx.core.MolgenisFile

Shorthand for db.query(MolgenisFile.class).

query(Database) - Static method in class org.molgenis.omx.core.RuntimeProperty

Shorthand for db.query(RuntimeProperty.class).

query(Database) - Static method in class org.molgenis.omx.observ.Category

Shorthand for db.query(Category.class).

query(Database) - Static method in class org.molgenis.omx.observ.Characteristic

Shorthand for db.query(Characteristic.class).

query(Database) - Static method in class org.molgenis.omx.observ.DataSet

Shorthand for db.query(DataSet.class).

query(Database) - Static method in class org.molgenis.omx.observ.ObservableFeature

Shorthand for db.query(ObservableFeature.class).

query(Database) - Static method in class org.molgenis.omx.observ.ObservationSet

Shorthand for db.query(ObservationSet.class).

query(Database) - Static method in class org.molgenis.omx.observ.ObservationTarget

Shorthand for db.query(ObservationTarget.class).

query(Database) - Static method in class org.molgenis.omx.observ.ObservedValue

Shorthand for db.query(ObservedValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.Protocol

Shorthand for db.query(Protocol.class).

query(Database) - Static method in class org.molgenis.omx.observ.Protocol_Features

Shorthand for db.query(Protocol_Features.class).

query(Database) - Static method in class org.molgenis.omx.observ.Protocol_Subprotocols

Shorthand for db.query(Protocol_Subprotocols.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Accession

Shorthand for db.query(Accession.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Individual

Shorthand for db.query(Individual.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Ontology

Shorthand for db.query(Ontology.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.OntologyTerm

Shorthand for db.query(OntologyTerm.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Panel

Shorthand for db.query(Panel.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Panel_Individuals

Shorthand for db.query(Panel_Individuals.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.PanelSource

Shorthand for db.query(PanelSource.class).

query(Database) - Static method in class org.molgenis.omx.observ.target.Species

Shorthand for db.query(Species.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.BoolValue

Shorthand for db.query(BoolValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.CategoricalValue

Shorthand for db.query(CategoricalValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.DateTimeValue

Shorthand for db.query(DateTimeValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.DateValue

Shorthand for db.query(DateValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.DecimalValue

Shorthand for db.query(DecimalValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.EmailValue

Shorthand for db.query(EmailValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.HtmlValue

Shorthand for db.query(HtmlValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.HyperlinkValue

Shorthand for db.query(HyperlinkValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.IntValue

Shorthand for db.query(IntValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.LongValue

Shorthand for db.query(LongValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.MrefValue

Shorthand for db.query(MrefValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.MrefValue_Value

Shorthand for db.query(MrefValue_Value.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.StringValue

Shorthand for db.query(StringValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.TextValue

Shorthand for db.query(TextValue.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.Value

Shorthand for db.query(Value.class).

query(Database) - Static method in class org.molgenis.omx.observ.value.XrefValue

Shorthand for db.query(XrefValue.class).

R

read(Integer) - Method in class org.molgenis.service.AccessionService

read(Integer) - Method in class org.molgenis.service.BoolValueService

read(Integer) - Method in class org.molgenis.service.CategoricalValueService

read(Integer) - Method in class org.molgenis.service.CategoryService

read(Integer) - Method in class org.molgenis.service.CharacteristicService

read(Integer) - Method in class org.molgenis.service.DataSetService

read(Integer) - Method in class org.molgenis.service.DateTimeValueService

read(Integer) - Method in class org.molgenis.service.DateValueService

read(Integer) - Method in class org.molgenis.service.DecimalValueService

read(Integer) - Method in class org.molgenis.service.EmailValueService

read(Integer) - Method in class org.molgenis.service.HtmlValueService

read(Integer) - Method in class org.molgenis.service.HyperlinkValueService

read(Integer) - Method in class org.molgenis.service.IndividualService

read(Integer) - Method in class org.molgenis.service.IntValueService

read(Integer) - Method in class org.molgenis.service.LongValueService

read(Integer) - Method in class org.molgenis.service.MolgenisFileService

read(Integer) - Method in class org.molgenis.service.MrefValueService

read(Integer) - Method in class org.molgenis.service.ObservableFeatureService

read(Integer) - Method in class org.molgenis.service.ObservationSetService

read(Integer) - Method in class org.molgenis.service.ObservationTargetService

read(Integer) - Method in class org.molgenis.service.ObservedValueService

read(Integer) - Method in class org.molgenis.service.OntologyService

read(Integer) - Method in class org.molgenis.service.OntologyTermService

read(Integer) - Method in class org.molgenis.service.PanelService

read(Integer) - Method in class org.molgenis.service.PanelSourceService

read(Integer) - Method in class org.molgenis.service.ProtocolService

read(Integer) - Method in class org.molgenis.service.RuntimePropertyService

read(Integer) - Method in class org.molgenis.service.SpeciesService

read(Integer) - Method in class org.molgenis.service.StringValueService

read(Integer) - Method in class org.molgenis.service.TextValueService

read(Integer) - Method in class org.molgenis.service.ValueService

read(Integer) - Method in class org.molgenis.service.XrefValueService

readAll() - Method in class org.molgenis.service.AccessionService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.AccessionService

readAll() - Method in class org.molgenis.service.BoolValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.BoolValueService

readAll() - Method in class org.molgenis.service.CategoricalValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.CategoricalValueService

readAll() - Method in class org.molgenis.service.CategoryService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.CategoryService

readAll() - Method in class org.molgenis.service.CharacteristicService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.CharacteristicService

readAll() - Method in class org.molgenis.service.DataSetService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.DataSetService

readAll() - Method in class org.molgenis.service.DateTimeValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.DateTimeValueService

readAll() - Method in class org.molgenis.service.DateValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.DateValueService

readAll() - Method in class org.molgenis.service.DecimalValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.DecimalValueService

readAll() - Method in class org.molgenis.service.EmailValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.EmailValueService

readAll() - Method in class org.molgenis.service.HtmlValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.HtmlValueService

readAll() - Method in class org.molgenis.service.HyperlinkValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.HyperlinkValueService

readAll() - Method in class org.molgenis.service.IndividualService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.IndividualService

readAll() - Method in class org.molgenis.service.IntValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.IntValueService

readAll() - Method in class org.molgenis.service.LongValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.LongValueService

readAll() - Method in class org.molgenis.service.MolgenisFileService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MolgenisFileService

readAll() - Method in class org.molgenis.service.MrefValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MrefValueService

readAll() - Method in class org.molgenis.service.ObservableFeatureService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ObservableFeatureService

readAll() - Method in class org.molgenis.service.ObservationSetService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ObservationSetService

readAll() - Method in class org.molgenis.service.ObservationTargetService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ObservationTargetService

readAll() - Method in class org.molgenis.service.ObservedValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ObservedValueService

readAll() - Method in class org.molgenis.service.OntologyService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.OntologyService

readAll() - Method in class org.molgenis.service.OntologyTermService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.OntologyTermService

readAll() - Method in class org.molgenis.service.PanelService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.PanelService

readAll() - Method in class org.molgenis.service.PanelSourceService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.PanelSourceService

readAll() - Method in class org.molgenis.service.ProtocolService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ProtocolService

readAll() - Method in class org.molgenis.service.RuntimePropertyService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.RuntimePropertyService

readAll() - Method in class org.molgenis.service.SpeciesService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.SpeciesService

readAll() - Method in class org.molgenis.service.StringValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.StringValueService

readAll() - Method in class org.molgenis.service.TextValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.TextValueService

readAll() - Method in class org.molgenis.service.ValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ValueService

readAll() - Method in class org.molgenis.service.XrefValueService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.XrefValueService

remove() - Method in class org.molgenis.omx.dataset.DataSetTableIterator

remove(List<E>) - Method in class org.molgenis.omx.decorators.MolgenisFileDecorator

removeFromCart(ShoppingCartController.FeaturesRequest) - Method in class org.molgenis.omx.cart.ShoppingCartController

Report - Class in org.molgenis.omx.services

Report() - Constructor for class org.molgenis.omx.services.Report

resolveForeignKeys(List<MolgenisEntity>) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

resolveForeignKeys(List<MolgenisFile>) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

resolveForeignKeys(List<RuntimeProperty>) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

resolveForeignKeys(List<Category>) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

resolveForeignKeys(List<Characteristic>) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

resolveForeignKeys(List<DataSet>) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

resolveForeignKeys(List<ObservableFeature>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

resolveForeignKeys(List<ObservationSet>) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

resolveForeignKeys(List<ObservationTarget>) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

resolveForeignKeys(List<ObservedValue>) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

resolveForeignKeys(List<Protocol_Features>) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

resolveForeignKeys(List<Protocol_Subprotocols>) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

resolveForeignKeys(List<Protocol>) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

resolveForeignKeys(List<Accession>) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

resolveForeignKeys(List<Individual>) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

resolveForeignKeys(List<Ontology>) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

resolveForeignKeys(List<OntologyTerm>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

resolveForeignKeys(List<Panel_Individuals>) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

resolveForeignKeys(List<Panel>) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

resolveForeignKeys(List<PanelSource>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

resolveForeignKeys(List<Species>) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

resolveForeignKeys(List<BoolValue>) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

resolveForeignKeys(List<CategoricalValue>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

resolveForeignKeys(List<DateTimeValue>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

resolveForeignKeys(List<DateValue>) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

resolveForeignKeys(List<DecimalValue>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

resolveForeignKeys(List<EmailValue>) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

resolveForeignKeys(List<HtmlValue>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

resolveForeignKeys(List<HyperlinkValue>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

resolveForeignKeys(List<IntValue>) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

resolveForeignKeys(List<LongValue>) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

resolveForeignKeys(List<MrefValue_Value>) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

resolveForeignKeys(List<MrefValue>) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

resolveForeignKeys(List<StringValue>) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

resolveForeignKeys(List<TextValue>) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

resolveForeignKeys(List<Value>) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

resolveForeignKeys(List<XrefValue>) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

RuntimeProperty - Class in org.molgenis.omx.core

RuntimeProperty: .

RuntimeProperty() - Constructor for class org.molgenis.omx.core.RuntimeProperty

RuntimeProperty(RuntimeProperty) - Constructor for class org.molgenis.omx.core.RuntimeProperty

copy constructor

RuntimePropertyEntityImporter - Class in org.molgenis.omx.core.db

Reads RuntimeProperty from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

RuntimePropertyEntityImporter() - Constructor for class org.molgenis.omx.core.db.RuntimePropertyEntityImporter

RuntimePropertyForm - Class in org.molgenis.omx.core.ui

A HtmlForm that is preloaded with all inputs for entity RuntimeProperty

RuntimePropertyForm() - Constructor for class org.molgenis.omx.core.ui.RuntimePropertyForm

RuntimePropertyForm(RuntimeProperty) - Constructor for class org.molgenis.omx.core.ui.RuntimePropertyForm

RuntimePropertyJpaMapper - Class in org.molgenis.omx.core.db

RuntimePropertyJpaMapper(Database) - Constructor for class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

RuntimePropertyService - Class in org.molgenis.service

RuntimePropertyService() - Constructor for class org.molgenis.service.RuntimePropertyService

S

saveFileAttachements(List<MolgenisEntity>, File) - Method in class org.molgenis.omx.core.db.MolgenisEntityJpaMapper

saveFileAttachements(List<MolgenisFile>, File) - Method in class org.molgenis.omx.core.db.MolgenisFileJpaMapper

saveFileAttachements(List<RuntimeProperty>, File) - Method in class org.molgenis.omx.core.db.RuntimePropertyJpaMapper

saveFileAttachements(List<Category>, File) - Method in class org.molgenis.omx.observ.db.CategoryJpaMapper

saveFileAttachements(List<Characteristic>, File) - Method in class org.molgenis.omx.observ.db.CharacteristicJpaMapper

saveFileAttachements(List<DataSet>, File) - Method in class org.molgenis.omx.observ.db.DataSetJpaMapper

saveFileAttachements(List<ObservableFeature>, File) - Method in class org.molgenis.omx.observ.db.ObservableFeatureJpaMapper

saveFileAttachements(List<ObservationSet>, File) - Method in class org.molgenis.omx.observ.db.ObservationSetJpaMapper

saveFileAttachements(List<ObservationTarget>, File) - Method in class org.molgenis.omx.observ.db.ObservationTargetJpaMapper

saveFileAttachements(List<ObservedValue>, File) - Method in class org.molgenis.omx.observ.db.ObservedValueJpaMapper

saveFileAttachements(List<Protocol_Features>, File) - Method in class org.molgenis.omx.observ.db.Protocol_FeaturesJpaMapper

saveFileAttachements(List<Protocol_Subprotocols>, File) - Method in class org.molgenis.omx.observ.db.Protocol_SubprotocolsJpaMapper

saveFileAttachements(List<Protocol>, File) - Method in class org.molgenis.omx.observ.db.ProtocolJpaMapper

saveFileAttachements(List<Accession>, File) - Method in class org.molgenis.omx.observ.target.db.AccessionJpaMapper

saveFileAttachements(List<Individual>, File) - Method in class org.molgenis.omx.observ.target.db.IndividualJpaMapper

saveFileAttachements(List<Ontology>, File) - Method in class org.molgenis.omx.observ.target.db.OntologyJpaMapper

saveFileAttachements(List<OntologyTerm>, File) - Method in class org.molgenis.omx.observ.target.db.OntologyTermJpaMapper

saveFileAttachements(List<Panel_Individuals>, File) - Method in class org.molgenis.omx.observ.target.db.Panel_IndividualsJpaMapper

saveFileAttachements(List<Panel>, File) - Method in class org.molgenis.omx.observ.target.db.PanelJpaMapper

saveFileAttachements(List<PanelSource>, File) - Method in class org.molgenis.omx.observ.target.db.PanelSourceJpaMapper

saveFileAttachements(List<Species>, File) - Method in class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

saveFileAttachements(List<BoolValue>, File) - Method in class org.molgenis.omx.observ.value.db.BoolValueJpaMapper

saveFileAttachements(List<CategoricalValue>, File) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueJpaMapper

saveFileAttachements(List<DateTimeValue>, File) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueJpaMapper

saveFileAttachements(List<DateValue>, File) - Method in class org.molgenis.omx.observ.value.db.DateValueJpaMapper

saveFileAttachements(List<DecimalValue>, File) - Method in class org.molgenis.omx.observ.value.db.DecimalValueJpaMapper

saveFileAttachements(List<EmailValue>, File) - Method in class org.molgenis.omx.observ.value.db.EmailValueJpaMapper

saveFileAttachements(List<HtmlValue>, File) - Method in class org.molgenis.omx.observ.value.db.HtmlValueJpaMapper

saveFileAttachements(List<HyperlinkValue>, File) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueJpaMapper

saveFileAttachements(List<IntValue>, File) - Method in class org.molgenis.omx.observ.value.db.IntValueJpaMapper

saveFileAttachements(List<LongValue>, File) - Method in class org.molgenis.omx.observ.value.db.LongValueJpaMapper

saveFileAttachements(List<MrefValue_Value>, File) - Method in class org.molgenis.omx.observ.value.db.MrefValue_ValueJpaMapper

saveFileAttachements(List<MrefValue>, File) - Method in class org.molgenis.omx.observ.value.db.MrefValueJpaMapper

saveFileAttachements(List<StringValue>, File) - Method in class org.molgenis.omx.observ.value.db.StringValueJpaMapper

saveFileAttachements(List<TextValue>, File) - Method in class org.molgenis.omx.observ.value.db.TextValueJpaMapper

saveFileAttachements(List<Value>, File) - Method in class org.molgenis.omx.observ.value.db.ValueJpaMapper

saveFileAttachements(List<XrefValue>, File) - Method in class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

SELECTIONCRITERIA - Static variable in class org.molgenis.omx.observ.target.PanelSource

set(Tuple, boolean) - Method in class org.molgenis.omx.core.MolgenisEntity

set(Tuple, boolean) - Method in class org.molgenis.omx.core.MolgenisFile

set(Tuple, boolean) - Method in class org.molgenis.omx.core.RuntimeProperty

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.Category

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.Characteristic

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.DataSet

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.ObservableFeature

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.ObservationSet

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.ObservationTarget

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.ObservedValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.Protocol

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.Protocol_Features

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Accession

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Individual

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Ontology

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.OntologyTerm

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Panel

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.PanelSource

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.target.Species

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.BoolValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.CategoricalValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.DateTimeValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.DateValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.DecimalValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.EmailValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.HtmlValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.IntValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.LongValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.MrefValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.StringValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.TextValue

set(Tuple, boolean) - Method in class org.molgenis.omx.observ.value.Value

set(Tuple, boolean) - 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.

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_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.

setClassName(String) - Method in class org.molgenis.omx.core.MolgenisEntity

Set the Full name of the entity.

setCurrentPanel(Panel) - Method in class org.molgenis.omx.observ.target.PanelSource

Set the Panel for which these sources are defined..

setCurrentPanel(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource

setCurrentPanel_Id(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource

Set foreign key for field currentPanel.

setCurrentPanel_Identifier(String) - Method in class org.molgenis.omx.observ.target.PanelSource

Set a pretty label for cross reference CurrentPanel to Panel.Id.

setDataSet(DataSet) - Method in class org.molgenis.omx.dataset.DataSetTable

setDataType(String) - Method in class org.molgenis.omx.observ.ObservableFeature

Set the (Optional) Reference to the technical data type.

setDb(Database) - Method in class org.molgenis.omx.dataset.DataSetTable

setDb(Database) - Method in class org.molgenis.omx.protocol.ProtocolTable

setDefinition(OntologyTerm) - Method in class org.molgenis.omx.observ.Category

Set the The category that is being measured in a specific way..

setDefinition(Integer) - Method in class org.molgenis.omx.observ.Category

setDefinition(OntologyTerm) - Method in class org.molgenis.omx.observ.ObservableFeature

Set the The concept that is being measured in a specific way..

setDefinition(Integer) - Method in class org.molgenis.omx.observ.ObservableFeature

setDefinition(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Set the (Optional) The definition of the term..

setDefinition_Id(Integer) - Method in class org.molgenis.omx.observ.Category

Set foreign key for field definition.

setDefinition_Id(Integer) - Method in class org.molgenis.omx.observ.ObservableFeature

Set foreign key for field definition.

setDefinition_Identifier(String) - Method in class org.molgenis.omx.observ.Category

Set a pretty label for cross reference Definition to OntologyTerm.Id.

setDefinition_Identifier(String) - Method in class org.molgenis.omx.observ.ObservableFeature

Set a pretty label for cross reference Definition to OntologyTerm.Id.

setDescription(String) - Method in class org.molgenis.omx.observ.Characteristic

Set the (Optional) Rudimentary meta data about the observable feature.

setEndTime(Date) - Method in class org.molgenis.omx.observ.DataSet

Set the (Optional) time when the protocol ended..

setExtension(String) - Method in class org.molgenis.omx.core.MolgenisFile

Set the The file extension.

setFather(Individual) - Method in class org.molgenis.omx.observ.target.Individual

Set the Refers to the father of the individual..

setFather(Integer) - Method in class org.molgenis.omx.observ.target.Individual

setFather_Id(Integer) - Method in class org.molgenis.omx.observ.target.Individual

Set foreign key for field father.

setFather_Identifier(String) - Method in class org.molgenis.omx.observ.target.Individual

Set a pretty label for cross reference Father to Individual.Id.

setFeature(ObservableFeature) - Method in class org.molgenis.omx.observ.ObservedValue

Set the References the ObservableFeature that this observation was made on.

setFeature(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

setFeature_Id(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

Set foreign key for field feature.

setFeature_Identifier(String) - Method in class org.molgenis.omx.observ.ObservedValue

Set a pretty label for cross reference Feature to ObservableFeature.Id.

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

setFeatures(ObservableFeature) - Method in class org.molgenis.omx.observ.Protocol_Features

Set the .

setFeatures(Integer) - Method in class org.molgenis.omx.observ.Protocol_Features

setFeatures_Id(Integer...) - Method in class org.molgenis.omx.observ.Protocol

setFeatures_Id(List<Integer>) - Method in class org.molgenis.omx.observ.Protocol

Set foreign key for field features.

setFeatures_Id(Integer) - Method in class org.molgenis.omx.observ.Protocol_Features

Set foreign key for field features.

setFeatures_Identifier(List<String>) - Method in class org.molgenis.omx.observ.Protocol

Update the foreign key Features This sets features to null until next database transaction.

setFeatures_Identifier(String) - Method in class org.molgenis.omx.observ.Protocol_Features

Set a pretty label for cross reference Features to ObservableFeature.Id.

setFeaturesProtocolCollection(Collection<Protocol>) - Method in class org.molgenis.omx.observ.ObservableFeature

setFileStorage(File) - Method in class org.molgenis.omx.services.Report

setFileStorage(String, Database) - 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

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.MolgenisEntity

Set the automatically generated internal id, only for internal use..

setId(Integer) - Method in class org.molgenis.omx.core.MolgenisFile

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.MolgenisFile

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

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.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

setIndividuals(Individual) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Set the .

setIndividuals(Integer) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

setIndividuals_Id(Integer...) - Method in class org.molgenis.omx.observ.target.Panel

setIndividuals_Id(List<Integer>) - Method in class org.molgenis.omx.observ.target.Panel

Set foreign key for field individuals.

setIndividuals_Id(Integer) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Set foreign key for field individuals.

setIndividuals_Identifier(List<String>) - Method in class org.molgenis.omx.observ.target.Panel

Update the foreign key Individuals This sets individuals to null until next database transaction.

setIndividuals_Identifier(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Set a pretty label for cross reference Individuals to Individual.Id.

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..

setMother(Individual) - Method in class org.molgenis.omx.observ.target.Individual

Set the Refers to the mother of the individual..

setMother(Integer) - Method in class org.molgenis.omx.observ.target.Individual

setMother_Id(Integer) - Method in class org.molgenis.omx.observ.target.Individual

Set foreign key for field mother.

setMother_Identifier(String) - Method in class org.molgenis.omx.observ.target.Individual

Set a pretty label for cross reference Mother to Individual.Id.

setMrefValue(MrefValue) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Set the .

setMrefValue(Integer) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

setMrefValue_Id(Integer) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Set foreign key for field mrefValue.

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.MolgenisFile

Set the human readible name, not necessary unique..

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 NumberOfIndividuals.

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(Integer) - Method in class org.molgenis.omx.observ.Category

setObservableFeature_Id(Integer) - Method in class org.molgenis.omx.observ.Category

Set foreign key for field observableFeature.

setObservableFeature_Identifier(String) - Method in class org.molgenis.omx.observ.Category

Set a pretty label for cross reference ObservableFeature to ObservableFeature.Id.

setObservationSet(ObservationSet) - Method in class org.molgenis.omx.observ.ObservedValue

Set the Reference to the observation.

setObservationSet(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

setObservationSet_Id(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

Set foreign key for field observationSet.

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..

setOntology(Integer) - Method in class org.molgenis.omx.observ.target.OntologyTerm

setOntology_Id(Integer) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Set foreign key for field ontology.

setOntology_Identifier(String) - Method in class org.molgenis.omx.observ.target.OntologyTerm

Set a pretty label for cross reference Ontology to Ontology.Id.

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 .

setPanel(Integer) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

setPanel_Id(Integer) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Set foreign key for field panel.

setPanel_Identifier(String) - Method in class org.molgenis.omx.observ.target.Panel_Individuals

Set a pretty label for cross reference Panel to Panel.Id.

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).

setPanelType(Integer) - Method in class org.molgenis.omx.observ.target.Panel

setPanelType_Id(Integer) - Method in class org.molgenis.omx.observ.target.Panel

Set foreign key for field panelType.

setPanelType_Identifier(String) - Method in class org.molgenis.omx.observ.target.Panel

Set a pretty label for cross reference PanelType to OntologyTerm.Id.

setPartOfDataSet(DataSet) - Method in class org.molgenis.omx.observ.ObservationSet

Set the DataSet this ValueSet is part of..

setPartOfDataSet(Integer) - Method in class org.molgenis.omx.observ.ObservationSet

setPartOfDataSet_Id(Integer) - Method in class org.molgenis.omx.observ.ObservationSet

Set foreign key for field partOfDataSet.

setPartOfDataSet_Identifier(String) - Method in class org.molgenis.omx.observ.ObservationSet

Set a pretty label for cross reference PartOfDataSet to DataSet.Id.

setProperty(String, String) - Method in class org.molgenis.omx.MolgenisDbSettings

setProtocol(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Features

Set the .

setProtocol(Integer) - Method in class org.molgenis.omx.observ.Protocol_Features

setProtocol(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set the .

setProtocol(Integer) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

setProtocol_Id(Integer) - Method in class org.molgenis.omx.observ.Protocol_Features

Set foreign key for field protocol.

setProtocol_Id(Integer) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set foreign key for field protocol.

setProtocol_Identifier(String) - Method in class org.molgenis.omx.observ.Protocol_Features

Set a pretty label for cross reference Protocol to Protocol.Id.

setProtocol_Identifier(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set a pretty label for cross reference Protocol to Protocol.Id.

setProtocolType(OntologyTerm) - Method in class org.molgenis.omx.observ.Protocol

Set the classification of protocol.

setProtocolType(Integer) - Method in class org.molgenis.omx.observ.Protocol

setProtocolType_Id(Integer) - Method in class org.molgenis.omx.observ.Protocol

Set foreign key for field protocolType.

setProtocolType_Identifier(String) - Method in class org.molgenis.omx.observ.Protocol

Set a pretty label for cross reference ProtocolType to OntologyTerm.Id.

setProtocolUsed(Protocol) - Method in class org.molgenis.omx.observ.DataSet

Set the Reference to the protocol that is being used (if available).

setProtocolUsed(Integer) - Method in class org.molgenis.omx.observ.DataSet

setProtocolUsed_Id(Integer) - Method in class org.molgenis.omx.observ.DataSet

Set foreign key for field protocolUsed.

setProtocolUsed_Identifier(String) - Method in class org.molgenis.omx.observ.DataSet

Set a pretty label for cross reference ProtocolUsed to Protocol.Id.

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.

setSourcePanel(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource

setSourcePanel_Id(Integer) - Method in class org.molgenis.omx.observ.target.PanelSource

Set foreign key for field sourcePanel.

setSourcePanel_Identifier(String) - Method in class org.molgenis.omx.observ.target.PanelSource

Set a pretty label for cross reference SourcePanel to Panel.Id.

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..

setSpecies(Integer) - Method in class org.molgenis.omx.observ.target.Panel

setSpecies_Id(Integer) - Method in class org.molgenis.omx.observ.target.Panel

Set foreign key for field species.

setSpecies_Identifier(String) - Method in class org.molgenis.omx.observ.target.Panel

Set a pretty label for cross reference Species to Species.Id.

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

setSubprotocols(Protocol) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set the .

setSubprotocols(Integer) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

setSubprotocols_Id(Integer...) - Method in class org.molgenis.omx.observ.Protocol

setSubprotocols_Id(List<Integer>) - Method in class org.molgenis.omx.observ.Protocol

Set foreign key for field subprotocols.

setSubprotocols_Id(Integer) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set foreign key for field subprotocols.

setSubprotocols_Identifier(List<String>) - Method in class org.molgenis.omx.observ.Protocol

Update the foreign key Subprotocols This sets subprotocols to null until next database transaction.

setSubprotocols_Identifier(String) - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

Set a pretty label for cross reference Subprotocols to Protocol.Id.

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.

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).

setUnit(Integer) - Method in class org.molgenis.omx.observ.ObservableFeature

setUnit_Id(Integer) - Method in class org.molgenis.omx.observ.ObservableFeature

Set foreign key for field unit.

setUnit_Identifier(String) - Method in class org.molgenis.omx.observ.ObservableFeature

Set a pretty label for cross reference Unit to OntologyTerm.Id.

setValue(String) - Method in class org.molgenis.omx.core.RuntimeProperty

Set the Value.

setValue(Value) - Method in class org.molgenis.omx.observ.ObservedValue

Set the The value observed.

setValue(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

setValue(Boolean) - Method in class org.molgenis.omx.observ.value.BoolValue

Set the Value.

setValue(Category) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Set the Value.

setValue(Integer) - Method in class org.molgenis.omx.observ.value.CategoricalValue

setValue(Date) - Method in class org.molgenis.omx.observ.value.DateTimeValue

Set the Value.

setValue(Date) - Method in class org.molgenis.omx.observ.value.DateValue

Set the Value.

setValue(String) - Method in class org.molgenis.omx.observ.value.DateValue

Set the Value.

setValue(Double) - Method in class org.molgenis.omx.observ.value.DecimalValue

Set the Value.

setValue(String) - Method in class org.molgenis.omx.observ.value.EmailValue

Set the Value.

setValue(String) - Method in class org.molgenis.omx.observ.value.HtmlValue

Set the Value.

setValue(String) - Method in class org.molgenis.omx.observ.value.HyperlinkValue

Set the Value.

setValue(Integer) - Method in class org.molgenis.omx.observ.value.IntValue

Set the Value.

setValue(Long) - Method in class org.molgenis.omx.observ.value.LongValue

Set the Value.

setValue(List<Characteristic>) - Method in class org.molgenis.omx.observ.value.MrefValue

Set the Value.

setValue(Characteristic...) - Method in class org.molgenis.omx.observ.value.MrefValue

setValue(Characteristic) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Set the .

setValue(Integer) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

setValue(String) - Method in class org.molgenis.omx.observ.value.StringValue

Set the Value.

setValue(String) - Method in class org.molgenis.omx.observ.value.TextValue

Set the Value.

setValue(Characteristic) - Method in class org.molgenis.omx.observ.value.XrefValue

Set the Value.

setValue(Integer) - Method in class org.molgenis.omx.observ.value.XrefValue

setValue_Id(Integer) - Method in class org.molgenis.omx.observ.ObservedValue

Set foreign key for field value.

setValue_Id(Integer) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Set foreign key for field value.

setValue_Id(Integer...) - Method in class org.molgenis.omx.observ.value.MrefValue

setValue_Id(List<Integer>) - Method in class org.molgenis.omx.observ.value.MrefValue

Set foreign key for field value.

setValue_Id(Integer) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Set foreign key for field value.

setValue_Id(Integer) - Method in class org.molgenis.omx.observ.value.XrefValue

Set foreign key for field value.

setValue_Identifier(String) - Method in class org.molgenis.omx.observ.value.CategoricalValue

Set a pretty label for cross reference Value to Category.Id.

setValue_Identifier(List<String>) - Method in class org.molgenis.omx.observ.value.MrefValue

Update the foreign key Value This sets value to null until next database transaction.

setValue_Identifier(String) - Method in class org.molgenis.omx.observ.value.MrefValue_Value

Set a pretty label for cross reference Value to Characteristic.Id.

setValue_Identifier(String) - Method in class org.molgenis.omx.observ.value.XrefValue

Set a pretty label for cross reference Value to Characteristic.Id.

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

shoppingCart() - Method in class org.molgenis.omx.OmxConfig

ShoppingCartController - Class in org.molgenis.omx.cart

ShoppingCartController() - Constructor for class org.molgenis.omx.cart.ShoppingCartController

SOURCEPANEL - Static variable in class org.molgenis.omx.observ.target.PanelSource

SOURCEPANEL_IDENTIFIER - 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

Species(Species) - Constructor for class org.molgenis.omx.observ.target.Species

copy constructor

SPECIES_IDENTIFIER - Static variable in class org.molgenis.omx.observ.target.Panel

SpeciesEntityImporter - Class in org.molgenis.omx.observ.target.db

Reads Species from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

SpeciesEntityImporter() - Constructor for class org.molgenis.omx.observ.target.db.SpeciesEntityImporter

SpeciesForm - Class in org.molgenis.omx.observ.target.ui

A HtmlForm that is preloaded with all inputs for entity Species

SpeciesForm() - Constructor for class org.molgenis.omx.observ.target.ui.SpeciesForm

SpeciesForm(Species) - Constructor for class org.molgenis.omx.observ.target.ui.SpeciesForm

SpeciesJpaMapper - Class in org.molgenis.omx.observ.target.db

SpeciesJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.target.db.SpeciesJpaMapper

SpeciesService - Class in org.molgenis.service

SpeciesService() - Constructor for class org.molgenis.service.SpeciesService

STARTTIME - Static variable in class org.molgenis.omx.observ.DataSet

StorageHandler - Class in org.molgenis.omx.services

StorageHandler(Database) - Constructor for class org.molgenis.omx.services.StorageHandler

On instantiation, build a simple report of the current state, without running actual validation yet.

strict - Variable in class org.molgenis.omx.decorators.MolgenisFileDecorator

StringValue - Class in org.molgenis.omx.observ.value

StringValue: .

StringValue() - Constructor for class org.molgenis.omx.observ.value.StringValue

StringValue(StringValue) - Constructor for class org.molgenis.omx.observ.value.StringValue

copy constructor

StringValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads StringValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

StringValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.StringValueEntityImporter

StringValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity StringValue

StringValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.StringValueForm

StringValueForm(StringValue) - Constructor for class org.molgenis.omx.observ.value.ui.StringValueForm

StringValueJpaMapper - Class in org.molgenis.omx.observ.value.db

StringValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.StringValueJpaMapper

StringValueService - Class in org.molgenis.service

StringValueService() - Constructor for class org.molgenis.service.StringValueService

SUBPROTOCOLS - Static variable in class org.molgenis.omx.observ.Protocol

SUBPROTOCOLS - Static variable in class org.molgenis.omx.observ.Protocol_Subprotocols

SUBPROTOCOLS_IDENTIFIER - Static variable in class org.molgenis.omx.observ.Protocol

SUBPROTOCOLS_IDENTIFIER - 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

TextValue(TextValue) - Constructor for class org.molgenis.omx.observ.value.TextValue

copy constructor

TextValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads TextValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

TextValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.TextValueEntityImporter

TextValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity TextValue

TextValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.TextValueForm

TextValueForm(TextValue) - Constructor for class org.molgenis.omx.observ.value.ui.TextValueForm

TextValueJpaMapper - Class in org.molgenis.omx.observ.value.db

TextValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.TextValueJpaMapper

TextValueService - Class in org.molgenis.service

TextValueService() - Constructor for class org.molgenis.service.TextValueService

TIME - Static variable in class org.molgenis.omx.observ.ObservationSet

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToBoolValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToCategoricalValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToDateTimeValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToDateValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToDecimalValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToEmailValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToHtmlValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToHyperlinkValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToIntValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToLongValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToMrefValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToStringValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToTextValueConverter

toCell(Value) - Method in interface org.molgenis.omx.converters.TupleToValueConverter

Returns the java type value contained by a value entity

toCell(Value) - Method in class org.molgenis.omx.converters.TupleToXrefValueConverter

toCell(Value) - Method in class org.molgenis.omx.converters.ValueConverter

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.MolgenisFile

toString(boolean) - Method in class org.molgenis.omx.core.MolgenisFile

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.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_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.utils.ValueCell

TupleToBoolValueConverter - Class in org.molgenis.omx.converters

TupleToBoolValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToBoolValueConverter

TupleToCategoricalValueConverter - Class in org.molgenis.omx.converters

TupleToCategoricalValueConverter(Database) - Constructor for class org.molgenis.omx.converters.TupleToCategoricalValueConverter

TupleToDateTimeValueConverter - Class in org.molgenis.omx.converters

TupleToDateTimeValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToDateTimeValueConverter

TupleToDateValueConverter - Class in org.molgenis.omx.converters

TupleToDateValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToDateValueConverter

TupleToDecimalValueConverter - Class in org.molgenis.omx.converters

TupleToDecimalValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToDecimalValueConverter

TupleToEmailValueConverter - Class in org.molgenis.omx.converters

TupleToEmailValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToEmailValueConverter

TupleToHtmlValueConverter - Class in org.molgenis.omx.converters

TupleToHtmlValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToHtmlValueConverter

TupleToHyperlinkValueConverter - Class in org.molgenis.omx.converters

TupleToHyperlinkValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToHyperlinkValueConverter

TupleToIntValueConverter - Class in org.molgenis.omx.converters

TupleToIntValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToIntValueConverter

TupleToLongValueConverter - Class in org.molgenis.omx.converters

TupleToLongValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToLongValueConverter

TupleToMrefValueConverter - Class in org.molgenis.omx.converters

TupleToMrefValueConverter(CharacteristicLoadingCache) - Constructor for class org.molgenis.omx.converters.TupleToMrefValueConverter

TupleToStringValueConverter - Class in org.molgenis.omx.converters

TupleToStringValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToStringValueConverter

TupleToTextValueConverter - Class in org.molgenis.omx.converters

TupleToTextValueConverter() - Constructor for class org.molgenis.omx.converters.TupleToTextValueConverter

TupleToValueConverter<S extends Value,T> - Interface in org.molgenis.omx.converters

TupleToXrefValueConverter - Class in org.molgenis.omx.converters

TupleToXrefValueConverter(CharacteristicLoadingCache) - Constructor for class org.molgenis.omx.converters.TupleToXrefValueConverter

TYPE_ - Static variable in class org.molgenis.omx.core.MolgenisEntity

U

UNIT - Static variable in class org.molgenis.omx.observ.ObservableFeature

UNIT_IDENTIFIER - Static variable in class org.molgenis.omx.observ.ObservableFeature

update(List<E>) - Method in class org.molgenis.omx.decorators.EmailValueDecorator

update(List<E>) - Method in class org.molgenis.omx.decorators.HyperlinkValueDecorator

update(List<E>) - Method in class org.molgenis.omx.decorators.MolgenisFileDecorator

update(Accession) - Method in class org.molgenis.service.AccessionService

update(BoolValue) - Method in class org.molgenis.service.BoolValueService

update(CategoricalValue) - Method in class org.molgenis.service.CategoricalValueService

update(Category) - Method in class org.molgenis.service.CategoryService

update(Characteristic) - Method in class org.molgenis.service.CharacteristicService

update(DataSet) - Method in class org.molgenis.service.DataSetService

update(DateTimeValue) - Method in class org.molgenis.service.DateTimeValueService

update(DateValue) - Method in class org.molgenis.service.DateValueService

update(DecimalValue) - Method in class org.molgenis.service.DecimalValueService

update(EmailValue) - Method in class org.molgenis.service.EmailValueService

update(HtmlValue) - Method in class org.molgenis.service.HtmlValueService

update(HyperlinkValue) - Method in class org.molgenis.service.HyperlinkValueService

update(Individual) - Method in class org.molgenis.service.IndividualService

update(IntValue) - Method in class org.molgenis.service.IntValueService

update(LongValue) - Method in class org.molgenis.service.LongValueService

update(MolgenisFile) - Method in class org.molgenis.service.MolgenisFileService

update(MrefValue) - Method in class org.molgenis.service.MrefValueService

update(ObservableFeature) - Method in class org.molgenis.service.ObservableFeatureService

update(ObservationSet) - Method in class org.molgenis.service.ObservationSetService

update(ObservationTarget) - Method in class org.molgenis.service.ObservationTargetService

update(ObservedValue) - Method in class org.molgenis.service.ObservedValueService

update(Ontology) - Method in class org.molgenis.service.OntologyService

update(OntologyTerm) - Method in class org.molgenis.service.OntologyTermService

update(Panel) - Method in class org.molgenis.service.PanelService

update(PanelSource) - Method in class org.molgenis.service.PanelSourceService

update(Protocol) - Method in class org.molgenis.service.ProtocolService

update(RuntimeProperty) - Method in class org.molgenis.service.RuntimePropertyService

update(Species) - Method in class org.molgenis.service.SpeciesService

update(StringValue) - Method in class org.molgenis.service.StringValueService

update(TextValue) - Method in class org.molgenis.service.TextValueService

update(Value) - Method in class org.molgenis.service.ValueService

update(XrefValue) - Method in class org.molgenis.service.XrefValueService

V

validate() - Method in class org.molgenis.omx.core.MolgenisEntity

validate() - Method in class org.molgenis.omx.core.MolgenisFile

validate() - Method in class org.molgenis.omx.core.RuntimeProperty

validate() - Method in class org.molgenis.omx.observ.Category

validate() - Method in class org.molgenis.omx.observ.Characteristic

validate() - Method in class org.molgenis.omx.observ.DataSet

validate() - Method in class org.molgenis.omx.observ.ObservableFeature

validate() - Method in class org.molgenis.omx.observ.ObservationSet

validate() - Method in class org.molgenis.omx.observ.ObservationTarget

validate() - Method in class org.molgenis.omx.observ.ObservedValue

validate() - Method in class org.molgenis.omx.observ.Protocol

validate() - Method in class org.molgenis.omx.observ.Protocol_Features

validate() - Method in class org.molgenis.omx.observ.Protocol_Subprotocols

validate() - Method in class org.molgenis.omx.observ.target.Accession

validate() - Method in class org.molgenis.omx.observ.target.Individual

validate() - Method in class org.molgenis.omx.observ.target.Ontology

validate() - Method in class org.molgenis.omx.observ.target.OntologyTerm

validate() - Method in class org.molgenis.omx.observ.target.Panel

validate() - Method in class org.molgenis.omx.observ.target.Panel_Individuals

validate() - Method in class org.molgenis.omx.observ.target.PanelSource

validate() - Method in class org.molgenis.omx.observ.target.Species

validate() - Method in class org.molgenis.omx.observ.value.BoolValue

validate() - Method in class org.molgenis.omx.observ.value.CategoricalValue

validate() - Method in class org.molgenis.omx.observ.value.DateTimeValue

validate() - Method in class org.molgenis.omx.observ.value.DateValue

validate() - Method in class org.molgenis.omx.observ.value.DecimalValue

validate() - Method in class org.molgenis.omx.observ.value.EmailValue

validate() - Method in class org.molgenis.omx.observ.value.HtmlValue

validate() - Method in class org.molgenis.omx.observ.value.HyperlinkValue

validate() - Method in class org.molgenis.omx.observ.value.IntValue

validate() - Method in class org.molgenis.omx.observ.value.LongValue

validate() - Method in class org.molgenis.omx.observ.value.MrefValue

validate() - Method in class org.molgenis.omx.observ.value.MrefValue_Value

validate() - Method in class org.molgenis.omx.observ.value.StringValue

validate() - Method in class org.molgenis.omx.observ.value.TextValue

validate() - Method in class org.molgenis.omx.observ.value.Value

validate() - Method in class org.molgenis.omx.observ.value.XrefValue

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(Database) - 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.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(Value) - Constructor for class org.molgenis.omx.observ.value.Value

copy constructor

VALUE - Static variable in class org.molgenis.omx.observ.value.XrefValue

VALUE_ID - Static variable in class org.molgenis.omx.observ.ObservedValue

VALUE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.value.CategoricalValue

VALUE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.value.MrefValue

VALUE_IDENTIFIER - Static variable in class org.molgenis.omx.observ.value.MrefValue_Value

VALUE_IDENTIFIER - 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

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(Database) - 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

ValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads Value from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.ValueEntityImporter

ValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity Value

ValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.ValueForm

ValueForm(Value) - Constructor for class org.molgenis.omx.observ.value.ui.ValueForm

ValueJpaMapper - Class in org.molgenis.omx.observ.value.db

ValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.ValueJpaMapper

ValueService - Class in org.molgenis.service

ValueService() - Constructor for class org.molgenis.service.ValueService

X

XrefValue - Class in org.molgenis.omx.observ.value

XrefValue: .

XrefValue() - Constructor for class org.molgenis.omx.observ.value.XrefValue

XrefValue(XrefValue) - Constructor for class org.molgenis.omx.observ.value.XrefValue

copy constructor

XrefValueEntityImporter - Class in org.molgenis.omx.observ.value.db

Reads XrefValue from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

XrefValueEntityImporter() - Constructor for class org.molgenis.omx.observ.value.db.XrefValueEntityImporter

XrefValueForm - Class in org.molgenis.omx.observ.value.ui

A HtmlForm that is preloaded with all inputs for entity XrefValue

XrefValueForm() - Constructor for class org.molgenis.omx.observ.value.ui.XrefValueForm

XrefValueForm(XrefValue) - Constructor for class org.molgenis.omx.observ.value.ui.XrefValueForm

XrefValueJpaMapper - Class in org.molgenis.omx.observ.value.db

XrefValueJpaMapper(Database) - Constructor for class org.molgenis.omx.observ.value.db.XrefValueJpaMapper

XrefValueService - Class in org.molgenis.service

XrefValueService() - Constructor for class org.molgenis.service.XrefValueService

_

__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 L M N O P Q R S T U V X _