Index (molgenis-app-omx 0.0.4 API)

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

A

AccessionController - Class in org.molgenis.controller
AccessionController() - Constructor for class org.molgenis.controller.AccessionController
AccessionSecurityDecorator<E extends Accession> - Class in org.molgenis.omx.observ.target.db: TODO add column level security filters
AccessionSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.study.db.StudyDataRequestSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.workflow.db.ObservationSetFlowSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.workflow.db.ProtocolFlowSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator
add(List<E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator
Address - Class in org.molgenis.jaxb: Java class for Address complex type.
Address() - Constructor for class org.molgenis.jaxb.Address
anatomicSource - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary
AnnotationAvailabilityProfile - Class in org.molgenis.jaxb: Java class for AnnotationAvailabilityProfile complex type.
AnnotationAvailabilityProfile() - Constructor for class org.molgenis.jaxb.AnnotationAvailabilityProfile
AnnotationAvailabilityProfile.ProvidesInformationTo - Class in org.molgenis.jaxb: Java class for anonymous complex type.
AnnotationAvailabilityProfile.ProvidesInformationTo() - Constructor for class org.molgenis.jaxb.AnnotationAvailabilityProfile.ProvidesInformationTo
annotationDrivenTransactionManager() - Method in class org.molgenis.DatabaseConfig
appName - Variable in class org.molgenis.servlet.UsedMolgenisOptions

B

BackgroundController - Class in org.molgenis.omx.controller: Controller that handles home page requests
BackgroundController(MolgenisSettings) - Constructor for class org.molgenis.omx.controller.BackgroundController
BbmriToOmxConverter - Class in org.molgenis.bbmri
BbmriToOmxConverter(String, String) - Constructor for class org.molgenis.bbmri.BbmriToOmxConverter
binder(WebDataBinder) - Method in class org.molgenis.controller.AccessionController
binder(WebDataBinder) - Method in class org.molgenis.controller.BoolValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.CategoricalValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.CategoryController
binder(WebDataBinder) - Method in class org.molgenis.controller.CharacteristicController
binder(WebDataBinder) - Method in class org.molgenis.controller.ChromosomeController
binder(WebDataBinder) - Method in class org.molgenis.controller.CloneController
binder(WebDataBinder) - Method in class org.molgenis.controller.DataSetController
binder(WebDataBinder) - Method in class org.molgenis.controller.DateTimeValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.DateValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.DecimalValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.DerivedTraitController
binder(WebDataBinder) - Method in class org.molgenis.controller.EmailValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.EnvironmentalFactorController
binder(WebDataBinder) - Method in class org.molgenis.controller.GeneController
binder(WebDataBinder) - Method in class org.molgenis.controller.GroupAuthorityController
binder(WebDataBinder) - Method in class org.molgenis.controller.HtmlValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.HyperlinkValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.IndividualController
binder(WebDataBinder) - Method in class org.molgenis.controller.InstituteController
binder(WebDataBinder) - Method in class org.molgenis.controller.IntValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.LongValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.MarkerController
binder(WebDataBinder) - Method in class org.molgenis.controller.MassPeakController
binder(WebDataBinder) - Method in class org.molgenis.controller.MetaboliteController
binder(WebDataBinder) - Method in class org.molgenis.controller.MolgenisEntityController
binder(WebDataBinder) - Method in class org.molgenis.controller.MolgenisFileController
binder(WebDataBinder) - Method in class org.molgenis.controller.MolgenisGroupController
binder(WebDataBinder) - Method in class org.molgenis.controller.MolgenisGroupMemberController
binder(WebDataBinder) - Method in class org.molgenis.controller.MolgenisUserController
binder(WebDataBinder) - Method in class org.molgenis.controller.MrefValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.NMRBinController
binder(WebDataBinder) - Method in class org.molgenis.controller.ObservableFeatureController
binder(WebDataBinder) - Method in class org.molgenis.controller.ObservationSetController
binder(WebDataBinder) - Method in class org.molgenis.controller.ObservationSetFlowController
binder(WebDataBinder) - Method in class org.molgenis.controller.ObservationTargetController
binder(WebDataBinder) - Method in class org.molgenis.controller.ObservedValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.OntologyController
binder(WebDataBinder) - Method in class org.molgenis.controller.OntologyTermController
binder(WebDataBinder) - Method in class org.molgenis.controller.PairedSampleController
binder(WebDataBinder) - Method in class org.molgenis.controller.PanelController
binder(WebDataBinder) - Method in class org.molgenis.controller.PanelSourceController
binder(WebDataBinder) - Method in class org.molgenis.controller.PatientController
binder(WebDataBinder) - Method in class org.molgenis.controller.PersonController
binder(WebDataBinder) - Method in class org.molgenis.controller.PersonRoleController
binder(WebDataBinder) - Method in class org.molgenis.controller.PolymorphismController
binder(WebDataBinder) - Method in class org.molgenis.controller.ProbeController
binder(WebDataBinder) - Method in class org.molgenis.controller.ProbeSetController
binder(WebDataBinder) - Method in class org.molgenis.controller.ProteinController
binder(WebDataBinder) - Method in class org.molgenis.controller.ProtocolController
binder(WebDataBinder) - Method in class org.molgenis.controller.ProtocolFlowController
binder(WebDataBinder) - Method in class org.molgenis.controller.RuntimePropertyController
binder(WebDataBinder) - Method in class org.molgenis.controller.SampleController
binder(WebDataBinder) - Method in class org.molgenis.controller.SNPController
binder(WebDataBinder) - Method in class org.molgenis.controller.SpeciesController
binder(WebDataBinder) - Method in class org.molgenis.controller.SpotController
binder(WebDataBinder) - Method in class org.molgenis.controller.StringValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.StudyDataRequestController
binder(WebDataBinder) - Method in class org.molgenis.controller.TextValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.TrackController
binder(WebDataBinder) - Method in class org.molgenis.controller.TranscriptController
binder(WebDataBinder) - Method in class org.molgenis.controller.UserAuthorityController
binder(WebDataBinder) - Method in class org.molgenis.controller.ValueController
binder(WebDataBinder) - Method in class org.molgenis.controller.VariantController
binder(WebDataBinder) - Method in class org.molgenis.controller.XrefValueController
bla(ExcelSheetReader, String) - Method in class org.molgenis.gids.tools.compare.ValidationFile
bla(CsvReader, String) - Method in class org.molgenis.gids.tools.compare.ValidationFile
BoolValueController - Class in org.molgenis.controller
BoolValueController() - Constructor for class org.molgenis.controller.BoolValueController
BoolValueSecurityDecorator<E extends BoolValue> - Class in org.molgenis.omx.observ.value.db: TODO add column level security filters
BoolValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

C

D

E

F

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.study.db.StudyDataRequestSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.workflow.db.ObservationSetFlowSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.workflow.db.ProtocolFlowSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator
find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.study.db.StudyDataRequestSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.workflow.db.ObservationSetFlowSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.workflow.db.ProtocolFlowSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator
findById(Object) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator
firstName - Variable in class org.molgenis.jaxb.Person
floorOrPremises - Variable in class org.molgenis.jaxb.Address
fullName - Variable in class org.molgenis.jaxb.Person

G

gender - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary
GeneController - Class in org.molgenis.controller
GeneController() - Constructor for class org.molgenis.controller.GeneController
GeneSecurityDecorator<E extends Gene> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
GeneSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.GeneSecurityDecorator
getAnatomicSource() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the anatomicSource property.
getCity() - Method in class org.molgenis.jaxb.Address: Gets the value of the city property.
getCollectionProtocol() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile.ProvidesInformationTo: Gets the value of the collectionProtocol property.
getCollectionProtocol() - Method in class org.molgenis.jaxb.CbmNode.Protocols: Gets the value of the collectionProtocol property.
getCollectionProtocol() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile.RestrictsAccessTo: Gets the value of the collectionProtocol property.
getCountry() - Method in class org.molgenis.jaxb.Address: Gets the value of the country property.
getDateLastUpdated() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the dateLastUpdated property.
getDateType() - Method in class org.molgenis.gids.tools.convertor.MakeObservableFeature
getDepartmentOrDivision() - Method in class org.molgenis.jaxb.Address: Gets the value of the departmentOrDivision property.
getDescribesPatientAge() - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Gets the value of the describesPatientAge property.
getDescription() - Method in class org.molgenis.gids.tools.convertor.MakeObservableFeature
getDiagnosis() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary.Receives: Gets the value of the diagnosis property.
getDiagnosisType() - Method in class org.molgenis.jaxb.Diagnosis: Gets the value of the diagnosisType property.
getEmailAddress() - Method in class org.molgenis.jaxb.Person: Gets the value of the emailAddress property.
getEndDate() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the endDate property.
getEnrolls() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the enrolls property.
getEntityName() - Method in class org.molgenis.jaxb.Address: Gets the value of the entityName property.
getEntityNumber() - Method in class org.molgenis.jaxb.Address: Gets the value of the entityNumber property.
getEthnicity() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the ethnicity property.
getFeatures_Identifier() - Method in class org.molgenis.gids.tools.convertor.MakeEntityNameAndIdentifier
getFirstName() - Method in class org.molgenis.jaxb.Person: Gets the value of the firstName property.
getFloorOrPremises() - Method in class org.molgenis.jaxb.Address: Gets the value of the floorOrPremises property.
getFullName() - Method in class org.molgenis.jaxb.Person: Gets the value of the fullName property.
getGender() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the gender property.
getHash() - Method in class org.molgenis.gids.tools.compare.ValidationFile
getHomepageURL() - Method in class org.molgenis.jaxb.Institution: Gets the value of the homepageURL property.
getId() - Method in class org.molgenis.jaxb.Address: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.Diagnosis: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.Organization: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.Person: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.Preservation: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.Race: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the id property.
getId() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the id property.
getIdentifier() - Method in class org.molgenis.gids.tools.convertor.MakeEntityNameAndIdentifier
getIdentifier() - Method in class org.molgenis.gids.tools.convertor.MakeObservableFeature
getIdentifier() - Method in class org.molgenis.gids.tools.convertor.MakeObservationTarget
getIdentifier() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the identifier property.
getInstitution() - Method in class org.molgenis.jaxb.CollectionProtocol.ResidesAt: Gets the value of the institution property.
getIsAppliedTo() - Method in class org.molgenis.jaxb.Preservation: Gets the value of the isAppliedTo property.
getIsAssignedTo() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the isAssignedTo property.
getIsClassifiedBy() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the isClassifiedBy property.
getIsConstrainedBy() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the isConstrainedBy property.
getIsLocatedAt() - Method in class org.molgenis.jaxb.SpecimenCollectionContact: Gets the value of the isLocatedAt property.
getLastName() - Method in class org.molgenis.jaxb.Person: Gets the value of the lastName property.
getListFiles() - Method in class org.molgenis.omx.controller.CbmToOmxConverterController
getListOfHeaders() - Method in class org.molgenis.gids.tools.compare.ValidationFile
getMakesAvailable() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the makesAvailable property.
getMiddleNameOrInitial() - Method in class org.molgenis.jaxb.Person: Gets the value of the middleNameOrInitial property.
getName() - Method in class org.molgenis.gids.tools.convertor.MakeEntityNameAndIdentifier
getName() - Method in class org.molgenis.gids.tools.convertor.MakeObservableFeature
getName() - Method in class org.molgenis.gids.tools.convertor.MakeObservationTarget
getName() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the name property.
getName() - Method in class org.molgenis.jaxb.Organization: Gets the value of the name property.
getOutputDir() - Method in class org.molgenis.omx.controller.CbmToOmxConverterController
getParticipantCollectionSummary() - Method in class org.molgenis.jaxb.CollectionProtocol.Enrolls: Gets the value of the participantCollectionSummary property.
getParticipantCount() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the participantCount property.
getPatientAgeGroupHigh() - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Gets the value of the patientAgeGroupHigh property.
getPatientAgeGroupLow() - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Gets the value of the patientAgeGroupLow property.
getPhone() - Method in class org.molgenis.jaxb.SpecimenCollectionContact: Gets the value of the phone property.
getPostOfficeBox() - Method in class org.molgenis.jaxb.Address: Gets the value of the postOfficeBox property.
getPreservationType() - Method in class org.molgenis.jaxb.Preservation: Gets the value of the preservationType property.
getProtocols() - Method in class org.molgenis.jaxb.CbmNode: Gets the value of the protocols property.
getProvides() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the provides property.
getProvidesInformationTo() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the providesInformationTo property.
getQualifiesPatientAgeAtSpecimenCollection() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the qualifiesPatientAgeAtSpecimenCollection property.
getRace() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary.IsClassifiedBy: Gets the value of the race property.
getRace() - Method in class org.molgenis.jaxb.Race: Gets the value of the race property.
getReceives() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Gets the value of the receives property.
getResidesAt() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the residesAt property.
getRestrictsAccessTo() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the restrictsAccessTo property.
getSource() - Method in class org.molgenis.jaxb.CbmNode: Gets the value of the source property.
getSpecimenCollectionSummary() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary.Provides: Gets the value of the specimenCollectionSummary property.
getSpecimenCollectionSummary() - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection.DescribesPatientAge: Gets the value of the specimenCollectionSummary property.
getSpecimenCollectionSummary() - Method in class org.molgenis.jaxb.Preservation.IsAppliedTo: Gets the value of the specimenCollectionSummary property.
getSpecimenCount() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the specimenCount property.
getSpecimenType() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the specimenType property.
getStartDate() - Method in class org.molgenis.jaxb.CollectionProtocol: Gets the value of the startDate property.
getState() - Method in class org.molgenis.jaxb.Address: Gets the value of the state property.
getStorageTemperatureInCentegrades() - Method in class org.molgenis.jaxb.Preservation: Gets the value of the storageTemperatureInCentegrades property.
getStreetOrThoroughfareExtensionName() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetOrThoroughfareExtensionName property.
getStreetOrThoroughfareNameAndType() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetOrThoroughfareNameAndType property.
getStreetOrThoroughfareNumber() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetOrThoroughfareNumber property.
getStreetOrThoroughfareSectionName() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetOrThoroughfareSectionName property.
getStreetPostDirectional() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetPostDirectional property.
getStreetPreDirectional() - Method in class org.molgenis.jaxb.Address: Gets the value of the streetPreDirectional property.
getUndergoes() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Gets the value of the undergoes property.
getZipCode() - Method in class org.molgenis.jaxb.Address: Gets the value of the zipCode property.
GroupAuthorityController - Class in org.molgenis.controller
GroupAuthorityController() - Constructor for class org.molgenis.controller.GroupAuthorityController
GroupAuthoritySecurityDecorator<E extends GroupAuthority> - Class in org.molgenis.omx.auth.db: TODO add column level security filters
GroupAuthoritySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

H

I

id - Variable in class org.molgenis.jaxb.Address
id - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile
id - Variable in class org.molgenis.jaxb.CollectionProtocol
id - Variable in class org.molgenis.jaxb.Diagnosis
id - Variable in class org.molgenis.jaxb.Organization
id - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary
id - Variable in class org.molgenis.jaxb.PatientAgeGroupAtCollection
id - Variable in class org.molgenis.jaxb.Person
id - Variable in class org.molgenis.jaxb.Preservation
id - Variable in class org.molgenis.jaxb.Race
id - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
id - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary
ID - Static variable in class org.molgenis.omx.controller.BackgroundController
ID - Static variable in class org.molgenis.omx.controller.CbmToOmxConverterController
ID - Static variable in class org.molgenis.omx.controller.ContactController
ID - Static variable in class org.molgenis.omx.controller.HomeController
ID - Static variable in class org.molgenis.omx.controller.NewsController
ID - Static variable in class org.molgenis.omx.controller.ReferencesController
identifier - Variable in class org.molgenis.jaxb.CollectionProtocol
importEntities(File, Database.DatabaseAction) - Method in class org.molgenis.EntitiesImporterImpl
importEntities(Repository<? extends Entity>, String, Database.DatabaseAction) - Method in class org.molgenis.EntitiesImporterImpl
importEntities(EntitySource, Database.DatabaseAction) - Method in class org.molgenis.EntitiesImporterImpl
IndividualController - Class in org.molgenis.controller
IndividualController() - Constructor for class org.molgenis.controller.IndividualController
IndividualSecurityDecorator<E extends Individual> - Class in org.molgenis.omx.observ.target.db: TODO add column level security filters
IndividualSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator
init(Model) - Method in class org.molgenis.omx.controller.BackgroundController
init(Model) - Method in class org.molgenis.omx.controller.CbmToOmxConverterController
init(Model) - Method in class org.molgenis.omx.controller.ContactController
init(Model) - Method in class org.molgenis.omx.controller.HomeController
init(Model) - Method in class org.molgenis.omx.controller.NewsController
init(Model) - Method in class org.molgenis.omx.controller.ReferencesController
InstituteController - Class in org.molgenis.controller
InstituteController() - Constructor for class org.molgenis.controller.InstituteController
InstituteSecurityDecorator<E extends Institute> - Class in org.molgenis.omx.auth.db: TODO add column level security filters
InstituteSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.InstituteSecurityDecorator
institution - Variable in class org.molgenis.jaxb.CollectionProtocol.ResidesAt
Institution - Class in org.molgenis.jaxb: Java class for Institution complex type.
Institution() - Constructor for class org.molgenis.jaxb.Institution
IntValueController - Class in org.molgenis.controller
IntValueController() - Constructor for class org.molgenis.controller.IntValueController
IntValueSecurityDecorator<E extends IntValue> - Class in org.molgenis.omx.observ.value.db: TODO add column level security filters
IntValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator
isAppliedTo - Variable in class org.molgenis.jaxb.Preservation
isAssignedTo - Variable in class org.molgenis.jaxb.CollectionProtocol
isAvailableToCommercialOrganizations - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
isAvailableToForeignInvestigators - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
isAvailableToOutsideInstitution - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
isClassifiedBy - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary
isCollaborationRequired - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
isConstrainedBy - Variable in class org.molgenis.jaxb.CollectionProtocol
isDatabasePopulated() - Method in class org.molgenis.omx.WebAppDatabasePopulatorServiceImpl
isHasAdditionalPatientDemographics() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasAdditionalPatientDemographics property.
isHasExposureHistory() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasExposureHistory property.
isHasFamilyHistory() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasFamilyHistory property.
isHasHistopathologicInformation() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasHistopathologicInformation property.
isHasLabData() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasLabData property.
isHasLongitudinalSpecimens() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasLongitudinalSpecimens property.
isHasMatchedSpecimens() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasMatchedSpecimens property.
isHasOutcomeInformation() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasOutcomeInformation property.
isHasParticipantsAvailableForFollowup() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasParticipantsAvailableForFollowup property.
isHasTreatmentInformation() - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Gets the value of the hasTreatmentInformation property.
isIsAvailableToCommercialOrganizations() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the isAvailableToCommercialOrganizations property.
isIsAvailableToForeignInvestigators() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the isAvailableToForeignInvestigators property.
isIsAvailableToOutsideInstitution() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the isAvailableToOutsideInstitution property.
isIsCollaborationRequired() - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Gets the value of the isCollaborationRequired property.
isLocatedAt - Variable in class org.molgenis.jaxb.SpecimenCollectionContact

J

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

L

lastName - Variable in class org.molgenis.jaxb.Person
load(File, File) - Method in class org.molgenis.cbm.CbmXmlParser
localEntityManagerFactoryBean() - Method in class org.molgenis.DatabaseConfig
LongValueController - Class in org.molgenis.controller
LongValueController() - Constructor for class org.molgenis.controller.LongValueController
LongValueSecurityDecorator<E extends LongValue> - Class in org.molgenis.omx.observ.value.db: TODO add column level security filters
LongValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

M

N

name - Variable in class org.molgenis.jaxb.CollectionProtocol
name - Variable in class org.molgenis.jaxb.Organization
NewsController - Class in org.molgenis.omx.controller: Controller that handles home page requests
NewsController(MolgenisSettings) - Constructor for class org.molgenis.omx.controller.NewsController
NMRBinController - Class in org.molgenis.controller
NMRBinController() - Constructor for class org.molgenis.controller.NMRBinController
NMRBinSecurityDecorator<E extends NMRBin> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
NMRBinSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

O

ObjectFactory - Class in org.molgenis.jaxb: This object contains factory methods for each Java content interface and Java element interface generated in the org.molgenis.jaxb package.
ObjectFactory() - Constructor for class org.molgenis.jaxb.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.molgenis.jaxb
ObservableFeatureController - Class in org.molgenis.controller
ObservableFeatureController() - Constructor for class org.molgenis.controller.ObservableFeatureController
ObservableFeatureSecurityDecorator<E extends ObservableFeature> - Class in org.molgenis.omx.observ.db: TODO add column level security filters
ObservableFeatureSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator
ObservationSetController - Class in org.molgenis.controller
ObservationSetController() - Constructor for class org.molgenis.controller.ObservationSetController
ObservationSetFlowController - Class in org.molgenis.controller
ObservationSetFlowController() - Constructor for class org.molgenis.controller.ObservationSetFlowController
ObservationSetFlowSecurityDecorator<E extends ObservationSetFlow> - Class in org.molgenis.omx.workflow.db: TODO add column level security filters
ObservationSetFlowSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.workflow.db.ObservationSetFlowSecurityDecorator
ObservationSetSecurityDecorator<E extends ObservationSet> - Class in org.molgenis.omx.observ.db: TODO add column level security filters
ObservationSetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator
ObservationTargetController - Class in org.molgenis.controller
ObservationTargetController() - Constructor for class org.molgenis.controller.ObservationTargetController
ObservationTargetSecurityDecorator<E extends ObservationTarget> - Class in org.molgenis.omx.observ.db: TODO add column level security filters
ObservationTargetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator
ObservedValueController - Class in org.molgenis.controller
ObservedValueController() - Constructor for class org.molgenis.controller.ObservedValueController
ObservedValueSecurityDecorator<E extends ObservedValue> - Class in org.molgenis.omx.observ.db: TODO add column level security filters
ObservedValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator
onStartup(ServletContext) - Method in class org.molgenis.omx.WebAppInitializer
OntologyController - Class in org.molgenis.controller
OntologyController() - Constructor for class org.molgenis.controller.OntologyController
OntologySecurityDecorator<E extends Ontology> - Class in org.molgenis.omx.observ.target.db: TODO add column level security filters
OntologySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.OntologySecurityDecorator
OntologyTermController - Class in org.molgenis.controller
OntologyTermController() - Constructor for class org.molgenis.controller.OntologyTermController
OntologyTermSecurityDecorator<E extends OntologyTerm> - Class in org.molgenis.omx.observ.target.db: TODO add column level security filters
OntologyTermSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator
org.molgenis - package org.molgenis
org.molgenis.bbmri - package org.molgenis.bbmri
org.molgenis.cbm - package org.molgenis.cbm
org.molgenis.controller - package org.molgenis.controller
org.molgenis.gids.tools.compare - package org.molgenis.gids.tools.compare
org.molgenis.gids.tools.convertor - package org.molgenis.gids.tools.convertor
org.molgenis.jaxb - package org.molgenis.jaxb
org.molgenis.omx - package org.molgenis.omx
org.molgenis.omx.auth.db - package org.molgenis.omx.auth.db
org.molgenis.omx.controller - package org.molgenis.omx.controller
org.molgenis.omx.core.db - package org.molgenis.omx.core.db
org.molgenis.omx.observ.db - package org.molgenis.omx.observ.db
org.molgenis.omx.observ.target.db - package org.molgenis.omx.observ.target.db
org.molgenis.omx.observ.value.db - package org.molgenis.omx.observ.value.db
org.molgenis.omx.patient.db - package org.molgenis.omx.patient.db
org.molgenis.omx.study.db - package org.molgenis.omx.study.db
org.molgenis.omx.workflow.db - package org.molgenis.omx.workflow.db
org.molgenis.omx.xgap.db - package org.molgenis.omx.xgap.db
org.molgenis.sampletab - package org.molgenis.sampletab
org.molgenis.servlet - package org.molgenis.servlet
Organization - Class in org.molgenis.jaxb: Java class for Organization complex type.
Organization() - Constructor for class org.molgenis.jaxb.Organization

P

Q

R

S

SampleController - Class in org.molgenis.controller
SampleController() - Constructor for class org.molgenis.controller.SampleController
SampleConverter - Class in org.molgenis.gids.tools.convertor
SampleConverter() - Constructor for class org.molgenis.gids.tools.convertor.SampleConverter
SampleSecurityDecorator<E extends Sample> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
SampleSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SampleSecurityDecorator
SampleTabOmxConverter - Class in org.molgenis.sampletab
SampleTabOmxConverter(String, String) - Constructor for class org.molgenis.sampletab.SampleTabOmxConverter
SecuredJpaDatabase - Class in org.molgenis
SecuredJpaDatabase(JDBCMetaDatabase) - Constructor for class org.molgenis.SecuredJpaDatabase
setAnatomicSource(String) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the anatomicSource property.
setCity(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the city property.
setCountry(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the country property.
setDateLastUpdated(XMLGregorianCalendar) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the dateLastUpdated property.
setDepartmentOrDivision(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the departmentOrDivision property.
setDescribesPatientAge(PatientAgeGroupAtCollection.DescribesPatientAge) - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Sets the value of the describesPatientAge property.
setDiagnosisType(String) - Method in class org.molgenis.jaxb.Diagnosis: Sets the value of the diagnosisType property.
setEmailAddress(String) - Method in class org.molgenis.jaxb.Person: Sets the value of the emailAddress property.
setEndDate(XMLGregorianCalendar) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the endDate property.
setEnrolls(CollectionProtocol.Enrolls) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the enrolls property.
setEntityName(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the entityName property.
setEntityNumber(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the entityNumber property.
setEthnicity(String) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the ethnicity property.
setFirstName(String) - Method in class org.molgenis.jaxb.Person: Sets the value of the firstName property.
setFloorOrPremises(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the floorOrPremises property.
setFullName(String) - Method in class org.molgenis.jaxb.Person: Sets the value of the fullName property.
setGender(String) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the gender property.
setHasAdditionalPatientDemographics(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasAdditionalPatientDemographics property.
setHasExposureHistory(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasExposureHistory property.
setHasFamilyHistory(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasFamilyHistory property.
setHasHistopathologicInformation(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasHistopathologicInformation property.
setHasLabData(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasLabData property.
setHasLongitudinalSpecimens(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasLongitudinalSpecimens property.
setHasMatchedSpecimens(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasMatchedSpecimens property.
setHasOutcomeInformation(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasOutcomeInformation property.
setHasParticipantsAvailableForFollowup(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasParticipantsAvailableForFollowup property.
setHasTreatmentInformation(Boolean) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the hasTreatmentInformation property.
setHomepageURL(String) - Method in class org.molgenis.jaxb.Institution: Sets the value of the homepageURL property.
setId(Integer) - Method in class org.molgenis.jaxb.Address: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.Diagnosis: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.Organization: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.Person: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.Preservation: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.Race: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the id property.
setId(Integer) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the id property.
setIdentifier(String) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the identifier property.
setIsAppliedTo(Preservation.IsAppliedTo) - Method in class org.molgenis.jaxb.Preservation: Sets the value of the isAppliedTo property.
setIsAssignedTo(SpecimenCollectionContact) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the isAssignedTo property.
setIsAvailableToCommercialOrganizations(Boolean) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the isAvailableToCommercialOrganizations property.
setIsAvailableToForeignInvestigators(Boolean) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the isAvailableToForeignInvestigators property.
setIsAvailableToOutsideInstitution(Boolean) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the isAvailableToOutsideInstitution property.
setIsClassifiedBy(ParticipantCollectionSummary.IsClassifiedBy) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the isClassifiedBy property.
setIsCollaborationRequired(Boolean) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the isCollaborationRequired property.
setIsConstrainedBy(SpecimenAvailabilitySummaryProfile) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the isConstrainedBy property.
setIsLocatedAt(Address) - Method in class org.molgenis.jaxb.SpecimenCollectionContact: Sets the value of the isLocatedAt property.
setLastName(String) - Method in class org.molgenis.jaxb.Person: Sets the value of the lastName property.
setMakesAvailable(AnnotationAvailabilityProfile) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the makesAvailable property.
setMiddleNameOrInitial(String) - Method in class org.molgenis.jaxb.Person: Sets the value of the middleNameOrInitial property.
setName(String) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the name property.
setName(String) - Method in class org.molgenis.jaxb.Organization: Sets the value of the name property.
setParticipantCount(Integer) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the participantCount property.
setPatientAgeGroupHigh(Integer) - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Sets the value of the patientAgeGroupHigh property.
setPatientAgeGroupLow(Integer) - Method in class org.molgenis.jaxb.PatientAgeGroupAtCollection: Sets the value of the patientAgeGroupLow property.
setPhone(String) - Method in class org.molgenis.jaxb.SpecimenCollectionContact: Sets the value of the phone property.
setPostOfficeBox(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the postOfficeBox property.
setPreservationType(String) - Method in class org.molgenis.jaxb.Preservation: Sets the value of the preservationType property.
setProtocols(CbmNode.Protocols) - Method in class org.molgenis.jaxb.CbmNode: Sets the value of the protocols property.
setProvides(ParticipantCollectionSummary.Provides) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the provides property.
setProvidesInformationTo(AnnotationAvailabilityProfile.ProvidesInformationTo) - Method in class org.molgenis.jaxb.AnnotationAvailabilityProfile: Sets the value of the providesInformationTo property.
setQualifiesPatientAgeAtSpecimenCollection(PatientAgeGroupAtCollection) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the qualifiesPatientAgeAtSpecimenCollection property.
setRace(String) - Method in class org.molgenis.jaxb.Race: Sets the value of the race property.
setReceives(ParticipantCollectionSummary.Receives) - Method in class org.molgenis.jaxb.ParticipantCollectionSummary: Sets the value of the receives property.
setResidesAt(CollectionProtocol.ResidesAt) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the residesAt property.
setRestrictsAccessTo(SpecimenAvailabilitySummaryProfile.RestrictsAccessTo) - Method in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile: Sets the value of the restrictsAccessTo property.
setSource(String) - Method in class org.molgenis.jaxb.CbmNode: Sets the value of the source property.
setSpecimenCount(Integer) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the specimenCount property.
setSpecimenType(String) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the specimenType property.
setStartDate(XMLGregorianCalendar) - Method in class org.molgenis.jaxb.CollectionProtocol: Sets the value of the startDate property.
setState(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the state property.
setStorageTemperatureInCentegrades(Integer) - Method in class org.molgenis.jaxb.Preservation: Sets the value of the storageTemperatureInCentegrades property.
setStreetOrThoroughfareExtensionName(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetOrThoroughfareExtensionName property.
setStreetOrThoroughfareNameAndType(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetOrThoroughfareNameAndType property.
setStreetOrThoroughfareNumber(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetOrThoroughfareNumber property.
setStreetOrThoroughfareSectionName(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetOrThoroughfareSectionName property.
setStreetPostDirectional(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetPostDirectional property.
setStreetPreDirectional(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the streetPreDirectional property.
setUndergoes(Preservation) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary: Sets the value of the undergoes property.
setZipCode(String) - Method in class org.molgenis.jaxb.Address: Sets the value of the zipCode property.
SNPController - Class in org.molgenis.controller
SNPController() - Constructor for class org.molgenis.controller.SNPController
SNPSecurityDecorator<E extends SNP> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
SNPSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SNPSecurityDecorator
source - Variable in class org.molgenis.jaxb.CbmNode
SpeciesController - Class in org.molgenis.controller
SpeciesController() - Constructor for class org.molgenis.controller.SpeciesController
SpeciesSecurityDecorator<E extends Species> - Class in org.molgenis.omx.observ.target.db: TODO add column level security filters
SpeciesSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator
SpecimenAvailabilitySummaryProfile - Class in org.molgenis.jaxb: Java class for SpecimenAvailabilitySummaryProfile complex type.
SpecimenAvailabilitySummaryProfile() - Constructor for class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile
SpecimenAvailabilitySummaryProfile.RestrictsAccessTo - Class in org.molgenis.jaxb: Java class for anonymous complex type.
SpecimenAvailabilitySummaryProfile.RestrictsAccessTo() - Constructor for class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile.RestrictsAccessTo
SpecimenCollectionContact - Class in org.molgenis.jaxb: Java class for SpecimenCollectionContact complex type.
SpecimenCollectionContact() - Constructor for class org.molgenis.jaxb.SpecimenCollectionContact
specimenCollectionSummary - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary.Provides
specimenCollectionSummary - Variable in class org.molgenis.jaxb.PatientAgeGroupAtCollection.DescribesPatientAge
specimenCollectionSummary - Variable in class org.molgenis.jaxb.Preservation.IsAppliedTo
SpecimenCollectionSummary - Class in org.molgenis.jaxb: Java class for SpecimenCollectionSummary complex type.
SpecimenCollectionSummary() - Constructor for class org.molgenis.jaxb.SpecimenCollectionSummary
specimenCount - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary
specimenType - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary
SpotController - Class in org.molgenis.controller
SpotController() - Constructor for class org.molgenis.controller.SpotController
SpotSecurityDecorator<E extends Spot> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
SpotSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SpotSecurityDecorator
startDate - Variable in class org.molgenis.jaxb.CollectionProtocol
state - Variable in class org.molgenis.jaxb.Address
storageTemperatureInCentegrades - Variable in class org.molgenis.jaxb.Preservation
streetOrThoroughfareExtensionName - Variable in class org.molgenis.jaxb.Address
streetOrThoroughfareNameAndType - Variable in class org.molgenis.jaxb.Address
streetOrThoroughfareNumber - Variable in class org.molgenis.jaxb.Address
streetOrThoroughfareSectionName - Variable in class org.molgenis.jaxb.Address
streetPostDirectional - Variable in class org.molgenis.jaxb.Address
streetPreDirectional - Variable in class org.molgenis.jaxb.Address
StringValueController - Class in org.molgenis.controller
StringValueController() - Constructor for class org.molgenis.controller.StringValueController
StringValueSecurityDecorator<E extends StringValue> - Class in org.molgenis.omx.observ.value.db: TODO add column level security filters
StringValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator
StudyDataRequestController - Class in org.molgenis.controller
StudyDataRequestController() - Constructor for class org.molgenis.controller.StudyDataRequestController
StudyDataRequestSecurityDecorator<E extends StudyDataRequest> - Class in org.molgenis.omx.study.db: TODO add column level security filters
StudyDataRequestSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.study.db.StudyDataRequestSecurityDecorator
studyDefinitionManagerService() - Method in class org.molgenis.omx.WebAppConfig

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validate(File) - Method in class org.molgenis.EntitiesValidatorImpl
ValidationChecker - Class in org.molgenis.gids.tools.compare: This script is created to compare 2 excelfiles.
ValidationChecker() - Constructor for class org.molgenis.gids.tools.compare.ValidationChecker
ValidationFile - Class in org.molgenis.gids.tools.compare: put in a hashmap
ValidationFile() - Constructor for class org.molgenis.gids.tools.compare.ValidationFile
ValueController - Class in org.molgenis.controller
ValueController() - Constructor for class org.molgenis.controller.ValueController
ValueSecurityDecorator<E extends Value> - Class in org.molgenis.omx.observ.value.db: TODO add column level security filters
ValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.ValueSecurityDecorator
VariantController - Class in org.molgenis.controller
VariantController() - Constructor for class org.molgenis.controller.VariantController
VariantSecurityDecorator<E extends Variant> - Class in org.molgenis.omx.xgap.db: TODO add column level security filters
VariantSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.VariantSecurityDecorator

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zipCode - Variable in class org.molgenis.jaxb.Address

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