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

A

addEntry(String, GafListValidationError) - Method in class org.molgenis.gaf.GafListValidationReport

addFreemarkerVariables(Map<String, Object>) - Method in class org.molgenis.app.WebAppConfig

addGlobalErrorMessage(String) - Method in class org.molgenis.gaf.GafListValidationReport

Address - Class in org.molgenis.jaxb

Java class for Address complex type.

Address() - Constructor for class org.molgenis.jaxb.Address

ALT - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

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.

annotationDrivenTransactionManager() - Method in class org.molgenis.DatabaseConfig

AppStartupIndexer - Class in org.molgenis.app

Reindexes all meta, mysql and jpa entities when the index is missing, at startup.

AppStartupIndexer(DataSource, SearchService, JpaRepositoryCollection) - Constructor for class org.molgenis.app.AppStartupIndexer

B

BackgroundController - Class in org.molgenis.app.controller

Controller that handles contact page requests

BackgroundController() - Constructor for class org.molgenis.app.controller.BackgroundController

C

CategoryParser - Class in org.molgenis.tools.compare

CategoryParser() - Constructor for class org.molgenis.tools.compare.CategoryParser

CbmNode - Class in org.molgenis.jaxb

Java class for CbmNode complex type.

CbmNode() - Constructor for class org.molgenis.jaxb.CbmNode

CbmNode.Protocols - Class in org.molgenis.jaxb

Java class for anonymous complex type.

CbmToOmxConverterController - Class in org.molgenis.app.controller

Controller that handles home page requests

CbmToOmxConverterController() - Constructor for class org.molgenis.app.controller.CbmToOmxConverterController

CbmXmlParser - Class in org.molgenis.cbm

CbmXmlParser() - Constructor for class org.molgenis.cbm.CbmXmlParser

check(String, String) - Method in class org.molgenis.tools.compare.CategoryParser

check(String, String, BufferedWriter) - Method in class org.molgenis.tools.compare.Validator

checkForMultipleConsults(String, String, PrintWriter) - Method in class org.molgenis.tools.compare.IBDParser

checkIfDouble(String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

CHROM - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

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

cleanUp() - Method in class org.molgenis.gaf.GafListValidationReport

collectionProtocol - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile.ProvidesInformationTo

collectionProtocol - Variable in class org.molgenis.jaxb.CbmNode.Protocols

CollectionProtocol - Class in org.molgenis.jaxb

Java class for CollectionProtocol complex type.

CollectionProtocol() - Constructor for class org.molgenis.jaxb.CollectionProtocol

collectionProtocol - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile.RestrictsAccessTo

CollectionProtocol.Enrolls - Class in org.molgenis.jaxb

Java class for anonymous complex type.

CollectionProtocol.ResidesAt - Class in org.molgenis.jaxb

Java class for anonymous complex type.

COLUMNS - Static variable in class org.molgenis.gaf.GafListValidator

compareDate(String, String, String, String, PrintWriter) - Method in class org.molgenis.tools.compare.IBDParser

compareRows(String, String, Entity, Entity, List<String>, BufferedWriter) - Static method in class org.molgenis.tools.compare.Validator

compareTo(GafListValidationError) - Method in class org.molgenis.gaf.GafListValidationError

configureUrlAuthorization(ExpressionUrlAuthorizationConfigurer<HttpSecurity>.ExpressionInterceptUrlRegistry) - Method in class org.molgenis.app.WebAppSecurityConfig

ContactController - Class in org.molgenis.app.controller

Controller that handles contact page requests

ContactController() - Constructor for class org.molgenis.app.controller.ContactController

convert(Part, HttpServletRequest, HttpServletResponse) - Method in class org.molgenis.app.controller.CbmToOmxConverterController

convert(InputStream, OutputStream, String, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

ConvertGidsMain - Class in org.molgenis.tools.gids.convertor

ConvertGidsMain() - Constructor for class org.molgenis.tools.gids.convertor.ConvertGidsMain

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

createAddress() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Address

createAddress(Address) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Address>}

createAnnotationAvailabilityProfile() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of AnnotationAvailabilityProfile

createAnnotationAvailabilityProfile(AnnotationAvailabilityProfile) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<AnnotationAvailabilityProfile>}

createAnnotationAvailabilityProfileProvidesInformationTo() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of AnnotationAvailabilityProfile.ProvidesInformationTo

createAnonymousUserAuthorities() - Method in class org.molgenis.app.WebAppSecurityConfig

createCbmNode() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of CbmNode

createCbmNode(CbmNode) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<CbmNode>}

createCbmNodeProtocols() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of CbmNode.Protocols

createCollectionProtocol() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of CollectionProtocol

createCollectionProtocol(CollectionProtocol) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<CollectionProtocol>}

createCollectionProtocolEnrolls() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of CollectionProtocol.Enrolls

createCollectionProtocolResidesAt() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of CollectionProtocol.ResidesAt

createDiagnosis() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Diagnosis

createDiagnosis(Diagnosis) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Diagnosis>}

createInstitution() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Institution

createInstitution(Institution) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Institution>}

createOrganization() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Organization

createOrganization(Organization) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Organization>}

createParticipantCollectionSummary() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of ParticipantCollectionSummary

createParticipantCollectionSummary(ParticipantCollectionSummary) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<ParticipantCollectionSummary>}

createParticipantCollectionSummaryIsClassifiedBy() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of ParticipantCollectionSummary.IsClassifiedBy

createParticipantCollectionSummaryProvides() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of ParticipantCollectionSummary.Provides

createParticipantCollectionSummaryReceives() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of ParticipantCollectionSummary.Receives

createPatientAgeGroupAtCollection() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of PatientAgeGroupAtCollection

createPatientAgeGroupAtCollection(PatientAgeGroupAtCollection) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<PatientAgeGroupAtCollection>}

createPatientAgeGroupAtCollectionDescribesPatientAge() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of PatientAgeGroupAtCollection.DescribesPatientAge

createPerson() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Person

createPerson(Person) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Person>}

createPreservation() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Preservation

createPreservation(Preservation) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Preservation>}

createPreservationIsAppliedTo() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Preservation.IsAppliedTo

createRace() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of Race

createRace(Race) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<Race>}

createSpecimenAvailabilitySummaryProfile() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of SpecimenAvailabilitySummaryProfile

createSpecimenAvailabilitySummaryProfile(SpecimenAvailabilitySummaryProfile) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<SpecimenAvailabilitySummaryProfile>}

createSpecimenAvailabilitySummaryProfileRestrictsAccessTo() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of SpecimenAvailabilitySummaryProfile.RestrictsAccessTo

createSpecimenCollectionContact() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of SpecimenCollectionContact

createSpecimenCollectionContact(SpecimenCollectionContact) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<SpecimenCollectionContact>}

createSpecimenCollectionSummary() - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of SpecimenCollectionSummary

createSpecimenCollectionSummary(SpecimenCollectionSummary) - Method in class org.molgenis.jaxb.ObjectFactory

Create an instance of JAXBElement<SpecimenCollectionSummary>}

D

DatabaseConfig - Class in org.molgenis

Database configuration

DatabaseConfig() - Constructor for class org.molgenis.DatabaseConfig

dataSource() - Method in class org.molgenis.DatabaseConfig

dateLastUpdated - Variable in class org.molgenis.jaxb.CollectionProtocol

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

describesPatientAge - Variable in class org.molgenis.jaxb.PatientAgeGroupAtCollection

DescribesPatientAge() - Constructor for class org.molgenis.jaxb.PatientAgeGroupAtCollection.DescribesPatientAge

Diagnosis - Class in org.molgenis.jaxb

Java class for Diagnosis complex type.

Diagnosis() - Constructor for class org.molgenis.jaxb.Diagnosis

diagnosis - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary.Receives

diagnosisType - Variable in class org.molgenis.jaxb.Diagnosis

E

emailAddress - Variable in class org.molgenis.jaxb.Person

emptySample() - Method in class org.molgenis.tools.gids.convertor.SampleConverter

endDate - Variable in class org.molgenis.jaxb.CollectionProtocol

enrolls - Variable in class org.molgenis.jaxb.CollectionProtocol

Enrolls() - Constructor for class org.molgenis.jaxb.CollectionProtocol.Enrolls

EntitiesImporterImpl - Class in org.molgenis

EntitiesImporterImpl(FileRepositoryCollectionFactory, EntityImportService) - Constructor for class org.molgenis.EntitiesImporterImpl

EntitiesValidatorImpl - Class in org.molgenis

EntitiesValidatorImpl(FileRepositoryCollectionFactory) - Constructor for class org.molgenis.EntitiesValidatorImpl

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

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

ethnicity - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary

F

firstName - Variable in class org.molgenis.jaxb.Person

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

freeMarkerConfigurer() - Method in class org.molgenis.app.WebAppConfig

fullName - Variable in class org.molgenis.jaxb.Person

G

GAF_LIST_VALIDATOR_EXAMPLE_PREFIX - Static variable in class org.molgenis.gaf.GafListValidator

RuntimeProperty.class.getSimpleName() + "_gafList.validator.example.";

GAF_LIST_VALIDATOR_PREFIX - Static variable in class org.molgenis.gaf.GafListValidator

RuntimeProperty.class.getSimpleName() + "_gafList.validator.";

GAFCol - Enum in org.molgenis.gaf

GAFLIST_ENTITYNAME - Static variable in class org.molgenis.gaf.GafListFileRepository

GafListFileImporterService - Class in org.molgenis.gaf

GafListFileImporterService() - Constructor for class org.molgenis.gaf.GafListFileImporterService

GafListFileRepository - Class in org.molgenis.gaf

Google spreadsheet repository that only exposes valid GAF list runs

GafListFileRepository(File, List<CellProcessor>, Character, GafListValidationReport) - Constructor for class org.molgenis.gaf.GafListFileRepository

GafListImporterController - Class in org.molgenis.gaf

GafListImporterController(GafListFileImporterService, MolgenisSettings) - Constructor for class org.molgenis.gaf.GafListImporterController

GafListValidationError - Class in org.molgenis.gaf

GafListValidationError(int, String, String, String) - Constructor for class org.molgenis.gaf.GafListValidationError

GafListValidationReport - Class in org.molgenis.gaf

GafListValidationReport() - Constructor for class org.molgenis.gaf.GafListValidationReport

GafListValidator - Class in org.molgenis.gaf

GafListValidator() - Constructor for class org.molgenis.gaf.GafListValidator

gender - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary

GeneticRepositoryMergerController - Class in org.molgenis.merge

GeneticRepositoryMergerController(RepositoryMerger, DataService, SearchService) - Constructor for class org.molgenis.merge.GeneticRepositoryMergerController

getAllColumnsNames() - Static method in enum org.molgenis.gaf.GAFCol

getAllRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

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.

getColName() - Method in class org.molgenis.gaf.GafListValidationError

getCountry() - Method in class org.molgenis.jaxb.Address

Gets the value of the country property.

getCrudRepositories() - Method in class org.molgenis.app.AppStartupIndexer

getDataSetIdentifier() - Method in class org.molgenis.gaf.GafListValidationReport

getDataSetName() - Method in class org.molgenis.gaf.GafListValidationReport

getDateLastUpdated() - Method in class org.molgenis.jaxb.CollectionProtocol

Gets the value of the dateLastUpdated property.

getDateType() - Method in class org.molgenis.tools.gids.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.tools.gids.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.

getEntitiesImportable() - Method in class org.molgenis.EntitiesImporterImpl

getEntityName() - Method in class org.molgenis.jaxb.Address

Gets the value of the entityName property.

getEntityNames() - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

getEntityNumber() - Method in class org.molgenis.jaxb.Address

Gets the value of the entityNumber property.

getEntries() - Method in class org.molgenis.gaf.GafListValidationReport

getEthnicity() - Method in class org.molgenis.jaxb.ParticipantCollectionSummary

Gets the value of the ethnicity property.

getFeatures_Identifier() - Method in class org.molgenis.tools.gids.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.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.jaxb.CollectionProtocol

Gets the value of the identifier property.

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getIdentifier() - Method in class org.molgenis.tools.gids.convertor.MakeObservationTarget

getInstitution() - Method in class org.molgenis.jaxb.CollectionProtocol.ResidesAt

Gets the value of the institution property.

getInvalidRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

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.app.controller.CbmToOmxConverterController

getListOfHeaders() - Method in class org.molgenis.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.

getMsg() - Method in class org.molgenis.gaf.GafListValidationError

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.

getName() - Method in class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

getName() - Method in class org.molgenis.tools.gids.convertor.MakeObservableFeature

getName() - Method in class org.molgenis.tools.gids.convertor.MakeObservationTarget

getOutputDir() - Method in class org.molgenis.app.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.

getRepositoryByEntityName(String) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

getRow() - Method in class org.molgenis.gaf.GafListValidationError

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.

getTempFile() - Method in class org.molgenis.gaf.GafListValidationReport

getTempFileName() - Method in class org.molgenis.gaf.GafListValidationReport

getTempFileOriginalName() - Method in class org.molgenis.gaf.GafListValidationReport

getUndergoes() - Method in class org.molgenis.jaxb.SpecimenCollectionSummary

Gets the value of the undergoes property.

getValidationGlobalErrorMessages() - Method in class org.molgenis.gaf.GafListValidationReport

getValidRunIds() - Method in class org.molgenis.gaf.GafListValidationReport

getValue() - Method in class org.molgenis.gaf.GafListValidationError

getZipCode() - Method in class org.molgenis.jaxb.Address

Gets the value of the zipCode property.

H

handleRuntimeException(RuntimeException) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

handleThrowable(Throwable) - Method in class org.molgenis.gaf.GafListImporterController

hasAdditionalPatientDemographics - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasErrors(String) - Method in class org.molgenis.gaf.GafListValidationReport

hasExposureHistory - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasFamilyHistory - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasGlobalErrors() - Method in class org.molgenis.gaf.GafListValidationReport

hasHistopathologicInformation - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasLabData - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasLongitudinalSpecimens - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasMatchedSpecimens - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasOutcomeInformation - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasParticipantsAvailableForFollowup - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

hasRunIdsErrors() - Method in class org.molgenis.gaf.GafListValidationReport

hasTreatmentInformation - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

HomeController - Class in org.molgenis.app.controller

Controller that handles home page requests

HomeController() - Constructor for class org.molgenis.app.controller.HomeController

homepageURL - Variable in class org.molgenis.jaxb.Institution

I

IBDParser - Class in org.molgenis.tools.compare

IBDParser() - Constructor for class org.molgenis.tools.compare.IBDParser

ID - Static variable in class org.molgenis.app.controller.BackgroundController

ID - Static variable in class org.molgenis.app.controller.CbmToOmxConverterController

ID - Static variable in class org.molgenis.app.controller.ContactController

ID - Static variable in class org.molgenis.app.controller.HomeController

ID - Static variable in class org.molgenis.app.controller.NewsController

ID - Static variable in class org.molgenis.app.controller.ReferencesController

ID - Static variable in class org.molgenis.gaf.GafListImporterController

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.merge.GeneticRepositoryMergerController

ID_FIELD - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

identifier - Variable in class org.molgenis.jaxb.CollectionProtocol

importGAFList(GafListValidationReport, String) - Method in class org.molgenis.gaf.GafListFileImporterService

importGAFList(Model) - Method in class org.molgenis.gaf.GafListImporterController

importGAFList(HttpServletRequest, Model) - Method in class org.molgenis.gaf.GafListImporterController

init(Model) - Method in class org.molgenis.app.controller.CbmToOmxConverterController

init(Model) - Method in class org.molgenis.gaf.GafListImporterController

init(Model) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

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

isAppliedTo - Variable in class org.molgenis.jaxb.Preservation

IsAppliedTo() - Constructor for class org.molgenis.jaxb.Preservation.IsAppliedTo

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

IsClassifiedBy() - Constructor for class org.molgenis.jaxb.ParticipantCollectionSummary.IsClassifiedBy

isCollaborationRequired - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile

isConstrainedBy - Variable in class org.molgenis.jaxb.CollectionProtocol

isDatabasePopulated() - Method in class org.molgenis.app.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

iterator() - Method in class org.molgenis.gaf.GafListFileRepository

J

JDBCMetaDatabase - Class in org.molgenis

This class is an in memory representation of the contents of your *_db.xml file Utility of this class is to allow for dynamic querying and/or user interfacing for example within a query tool or a security module.

JDBCMetaDatabase() - Constructor for class org.molgenis.JDBCMetaDatabase

jpaDialect() - Method in class org.molgenis.DatabaseConfig

JpaRepositoryCollection - Class in org.molgenis.data.jpa

JpaRepositoryCollection() - Constructor for class org.molgenis.data.jpa.JpaRepositoryCollection

jpaVendorAdapter() - Method in class org.molgenis.DatabaseConfig

K

KEY_GAF_LIST_DATASET_IDENTIFIER - Static variable in class org.molgenis.gaf.GafListImporterController

KEY_GAF_LIST_PROTOCOL_NAME - Static variable in class org.molgenis.gaf.GafListImporterController

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

M

main(String[]) - Static method in class org.molgenis.sampletab.SampleTabOmxConverter

main(String[]) - Static method in class org.molgenis.tools.compare.CategoryParser

main(String[]) - Static method in class org.molgenis.tools.compare.IBDParser

main(String[]) - Static method in class org.molgenis.tools.compare.Validator

main(String[]) - Static method in class org.molgenis.tools.gids.convertor.ConvertGidsMain

MakeEntityNameAndIdentifier - Class in org.molgenis.tools.gids.convertor

MakeEntityNameAndIdentifier(String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

MakeEntityNameAndIdentifier(String, String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeEntityNameAndIdentifier

MakeObservableFeature - Class in org.molgenis.tools.gids.convertor

MakeObservableFeature(String, String, String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeObservableFeature

MakeObservationTarget - Class in org.molgenis.tools.gids.convertor

MakeObservationTarget(String, String) - Constructor for class org.molgenis.tools.gids.convertor.MakeObservationTarget

makesAvailable - Variable in class org.molgenis.jaxb.CollectionProtocol

merge(String, String[]) - Method in class org.molgenis.merge.GeneticRepositoryMergerController

middleNameOrInitial - Variable in class org.molgenis.jaxb.Person

mkmetadataExcelFile(ArrayList<String>) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileDataSet(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileObservableFeature(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

mkMetadataFileProtocol(WritableFactory, String) - Method in class org.molgenis.tools.gids.convertor.SampleConverter

molgenisAccessDecisionVoter() - Method in class org.molgenis.app.WebAppSecurityConfig

N

name - Variable in class org.molgenis.jaxb.CollectionProtocol

name - Variable in class org.molgenis.jaxb.Organization

NewsController - Class in org.molgenis.app.controller

Controller that handles news page requests

NewsController() - Constructor for class org.molgenis.app.controller.NewsController

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

onStartup(ServletContext) - Method in class org.molgenis.app.WebAppInitializer

org.molgenis - package org.molgenis

org.molgenis.app - package org.molgenis.app

org.molgenis.app.controller - package org.molgenis.app.controller

org.molgenis.cbm - package org.molgenis.cbm

org.molgenis.data.jpa - package org.molgenis.data.jpa

org.molgenis.gaf - package org.molgenis.gaf

org.molgenis.jaxb - package org.molgenis.jaxb

org.molgenis.merge - package org.molgenis.merge

org.molgenis.sampletab - package org.molgenis.sampletab

org.molgenis.tools.compare - package org.molgenis.tools.compare

org.molgenis.tools.gids.convertor - package org.molgenis.tools.gids.convertor

Organization - Class in org.molgenis.jaxb

Java class for Organization complex type.

Organization() - Constructor for class org.molgenis.jaxb.Organization

P

participantCollectionSummary - Variable in class org.molgenis.jaxb.CollectionProtocol.Enrolls

ParticipantCollectionSummary - Class in org.molgenis.jaxb

Java class for ParticipantCollectionSummary complex type.

ParticipantCollectionSummary() - Constructor for class org.molgenis.jaxb.ParticipantCollectionSummary

ParticipantCollectionSummary.IsClassifiedBy - Class in org.molgenis.jaxb

Java class for anonymous complex type.

ParticipantCollectionSummary.Provides - Class in org.molgenis.jaxb

Java class for anonymous complex type.

ParticipantCollectionSummary.Receives - Class in org.molgenis.jaxb

Java class for anonymous complex type.

participantCount - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary

PatientAgeGroupAtCollection - Class in org.molgenis.jaxb

Java class for PatientAgeGroupAtCollection complex type.

PatientAgeGroupAtCollection() - Constructor for class org.molgenis.jaxb.PatientAgeGroupAtCollection

PatientAgeGroupAtCollection.DescribesPatientAge - Class in org.molgenis.jaxb

Java class for anonymous complex type.

patientAgeGroupHigh - Variable in class org.molgenis.jaxb.PatientAgeGroupAtCollection

patientAgeGroupLow - Variable in class org.molgenis.jaxb.PatientAgeGroupAtCollection

Person - Class in org.molgenis.jaxb

Java class for Person complex type.

Person() - Constructor for class org.molgenis.jaxb.Person

phone - Variable in class org.molgenis.jaxb.SpecimenCollectionContact

populateDatabase() - Method in class org.molgenis.app.WebAppDatabasePopulatorServiceImpl

populateStatusImportedRuns() - Method in class org.molgenis.gaf.GafListValidationReport

POS - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

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

Preservation - Class in org.molgenis.jaxb

Java class for Preservation complex type.

Preservation() - Constructor for class org.molgenis.jaxb.Preservation

Preservation.IsAppliedTo - Class in org.molgenis.jaxb

Java class for anonymous complex type.

preservationType - Variable in class org.molgenis.jaxb.Preservation

printAsList(Map<String, List<String>>) - Method in class org.molgenis.tools.compare.CategoryParser

printForCategoryTab(Map<String, List<String>>) - Method in class org.molgenis.tools.compare.CategoryParser

protocols - Variable in class org.molgenis.jaxb.CbmNode

Protocols() - Constructor for class org.molgenis.jaxb.CbmNode.Protocols

provides - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary

Provides() - Constructor for class org.molgenis.jaxb.ParticipantCollectionSummary.Provides

providesInformationTo - Variable in class org.molgenis.jaxb.AnnotationAvailabilityProfile

ProvidesInformationTo() - Constructor for class org.molgenis.jaxb.AnnotationAvailabilityProfile.ProvidesInformationTo

Q

qualifiesPatientAgeAtSpecimenCollection - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary

R

race - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary.IsClassifiedBy

Race - Class in org.molgenis.jaxb

Java class for Race complex type.

Race() - Constructor for class org.molgenis.jaxb.Race

race - Variable in class org.molgenis.jaxb.Race

readFile(Repository, String, String) - Method in class org.molgenis.tools.compare.ValidationFile

receives - Variable in class org.molgenis.jaxb.ParticipantCollectionSummary

Receives() - Constructor for class org.molgenis.jaxb.ParticipantCollectionSummary.Receives

REF - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

ReferencesController - Class in org.molgenis.app.controller

Controller that handles references page requests

ReferencesController() - Constructor for class org.molgenis.app.controller.ReferencesController

residesAt - Variable in class org.molgenis.jaxb.CollectionProtocol

ResidesAt() - Constructor for class org.molgenis.jaxb.CollectionProtocol.ResidesAt

restrictsAccessTo - Variable in class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile

RestrictsAccessTo() - Constructor for class org.molgenis.jaxb.SpecimenAvailabilitySummaryProfile.RestrictsAccessTo

roleHierarchy() - Method in class org.molgenis.app.WebAppSecurityConfig

S

SampleConverter - Class in org.molgenis.tools.gids.convertor

SampleConverter() - Constructor for class org.molgenis.tools.gids.convertor.SampleConverter

SampleTabOmxConverter - Class in org.molgenis.sampletab

SampleTabOmxConverter(String, String, String) - Constructor for class org.molgenis.sampletab.SampleTabOmxConverter

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.

setDataSetIdentifier(String) - Method in class org.molgenis.gaf.GafListValidationReport

setDataSetName(String) - Method in class org.molgenis.gaf.GafListValidationReport

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.

setDiseaseMappingRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setDiseaseRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setFreemarkerTemplateRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setGroupAuthorityRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setImportRunRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setMolgenisGroupMemberRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisGroupRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisTokenRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setMolgenisUserRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setRuntimePropertyRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

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.

setTempFile(File) - Method in class org.molgenis.gaf.GafListValidationReport

setTempFileName(String) - Method in class org.molgenis.gaf.GafListValidationReport

setTempFileOriginalName(String) - Method in class org.molgenis.gaf.GafListValidationReport

setUndergoes(Preservation) - Method in class org.molgenis.jaxb.SpecimenCollectionSummary

Sets the value of the undergoes property.

setUserAuthorityRepository(CrudRepository) - Method in class org.molgenis.data.jpa.JpaRepositoryCollection

setZipCode(String) - Method in class org.molgenis.jaxb.Address

Sets the value of the zipCode property.

source - Variable in class org.molgenis.jaxb.CbmNode

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.

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

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

T

toString() - Method in enum org.molgenis.gaf.GAFCol

toString() - Method in class org.molgenis.gaf.GafListValidationError

toString() - Method in class org.molgenis.gaf.GafListValidationReport

toStringHtml() - Method in class org.molgenis.gaf.GafListValidationError

toStringHtml() - Method in class org.molgenis.gaf.GafListValidationReport

transactionManager() - Method in class org.molgenis.DatabaseConfig

U

undergoes - Variable in class org.molgenis.jaxb.SpecimenCollectionSummary

uploadCsvFile(MultipartFile) - Method in class org.molgenis.gaf.GafListValidationReport

URI - Static variable in class org.molgenis.app.controller.BackgroundController

URI - Static variable in class org.molgenis.app.controller.CbmToOmxConverterController

URI - Static variable in class org.molgenis.app.controller.ContactController

URI - Static variable in class org.molgenis.app.controller.HomeController

URI - Static variable in class org.molgenis.app.controller.NewsController

URI - Static variable in class org.molgenis.app.controller.ReferencesController

URI - Static variable in class org.molgenis.gaf.GafListImporterController

URI - Static variable in class org.molgenis.merge.GeneticRepositoryMergerController

V

validate(File) - Method in class org.molgenis.EntitiesValidatorImpl

validate(GafListValidationReport, Repository, List<String>) - Method in class org.molgenis.gaf.GafListValidator

validateGAFList(GafListValidationReport, MultipartFile) - Method in class org.molgenis.gaf.GafListFileImporterService

validateGAFList(Model) - Method in class org.molgenis.gaf.GafListImporterController

validateGAFList(HttpServletRequest, MultipartFile, Model) - Method in class org.molgenis.gaf.GafListImporterController

ValidationFile - Class in org.molgenis.tools.compare

put in a hashmap

ValidationFile() - Constructor for class org.molgenis.tools.compare.ValidationFile

Validator - Class in org.molgenis.tools.compare

This script is created to compare 2 excelfiles.

Validator() - Constructor for class org.molgenis.tools.compare.Validator

valueOf(String) - Static method in enum org.molgenis.gaf.GAFCol

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.gaf.GAFCol

Returns an array containing the constants of this enum type, in the order they are declared.

W

WebAppConfig - Class in org.molgenis.app

WebAppConfig() - Constructor for class org.molgenis.app.WebAppConfig

WebAppDatabasePopulatorServiceImpl - Class in org.molgenis.app

WebAppDatabasePopulatorServiceImpl(DataService, MolgenisSecurityWebAppDatabasePopulatorService) - Constructor for class org.molgenis.app.WebAppDatabasePopulatorServiceImpl

WebAppInitializer - Class in org.molgenis.app

WebAppInitializer() - Constructor for class org.molgenis.app.WebAppInitializer

WebAppSecurityConfig - Class in org.molgenis.app

WebAppSecurityConfig() - Constructor for class org.molgenis.app.WebAppSecurityConfig

Z

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

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