Uses of Interface
org.molgenis.data.annotation.core.RepositoryAnnotator

Packages that use RepositoryAnnotator

Package	Description
org.molgenis.data.annotation.core
org.molgenis.data.annotation.core.entity.impl
org.molgenis.data.annotation.core.entity.impl.framework
org.molgenis.data.annotation.core.entity.impl.hpo
org.molgenis.data.annotation.core.entity.impl.omim
org.molgenis.data.annotation.core.entity.impl.snpeff
org.molgenis.data.annotation.core.utils
org.molgenis.data.annotation.web

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core

Classes in org.molgenis.data.annotation.core that implement RepositoryAnnotator

Modifier and Type	Class and Description
class	AbstractRepositoryAnnotator
class	AbstractRepositoryEntityAnnotator
class	EffectBasedAnnotator Annotator that annotates the "effects" entities rather than the variants themself

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.entity.impl

Methods in org.molgenis.data.annotation.core.entity.impl that return RepositoryAnnotator

Modifier and Type	Method and Description
RepositoryAnnotator	CaddAnnotator.cadd()
RepositoryAnnotator	CGDAnnotator.cgd()
RepositoryAnnotator	ClinvarAnnotator.clinvar()
RepositoryAnnotator	DannAnnotator.dann()
RepositoryAnnotator	ExacAnnotator.exac()
RepositoryAnnotator	FitConAnnotator.fitcon()
RepositoryAnnotator	GoNLAnnotator.gonl()
RepositoryAnnotator	ThousandGenomesAnnotator.thousandGenomes()

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.entity.impl.framework

Classes in org.molgenis.data.annotation.core.entity.impl.framework that implement RepositoryAnnotator

Modifier and Type	Class and Description
class	RepositoryAnnotatorImpl

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.entity.impl.hpo

Methods in org.molgenis.data.annotation.core.entity.impl.hpo that return RepositoryAnnotator

Modifier and Type	Method and Description
RepositoryAnnotator	HPOAnnotator.hpo()

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.entity.impl.omim

Methods in org.molgenis.data.annotation.core.entity.impl.omim that return RepositoryAnnotator

Modifier and Type	Method and Description
RepositoryAnnotator	OmimAnnotator.omim()

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.entity.impl.snpeff

Classes in org.molgenis.data.annotation.core.entity.impl.snpeff that implement RepositoryAnnotator

Modifier and Type	Class and Description
class	SnpEffRepositoryAnnotator

Methods in org.molgenis.data.annotation.core.entity.impl.snpeff that return RepositoryAnnotator

Modifier and Type	Method and Description
RepositoryAnnotator	SnpEffAnnotator.snpEff()

Uses of RepositoryAnnotator in org.molgenis.data.annotation.core.utils

Methods in org.molgenis.data.annotation.core.utils that return types with arguments of type RepositoryAnnotator

Modifier and Type	Method and Description
Queue<RepositoryAnnotator>	AnnotatorDependencyOrderResolver.getAnnotatorSelectionDependencyList(List<RepositoryAnnotator> availableAnnotatorList, List<RepositoryAnnotator> requestedAnnotatorList, Repository<Entity> repo, EntityTypeFactory entityTypeFactory)

Methods in org.molgenis.data.annotation.core.utils with parameters of type RepositoryAnnotator

Modifier and Type	Method and Description
static EntityType	AnnotatorUtils.addAnnotatorMetaDataToRepositories(EntityType entityType, AttributeFactory attributeFactory, RepositoryAnnotator annotator) Adds a new compound attribute to an existing CrudRepository
static String	CmdLineAnnotatorUtils.annotate(RepositoryAnnotator annotator, VcfAttributes vcfAttributes, EntityTypeFactory entityTypeFactory, AttributeFactory attributeFactory, EffectStructureConverter effectStructureConverter, File inputVcfFile, File outputVCFFile, List<String> attributesToInclude, boolean update) Adds a new compound attribute to an existing CrudRepository

Method parameters in org.molgenis.data.annotation.core.utils with type arguments of type RepositoryAnnotator

Modifier and Type	Method and Description
Queue<RepositoryAnnotator>	AnnotatorDependencyOrderResolver.getAnnotatorSelectionDependencyList(List<RepositoryAnnotator> availableAnnotatorList, List<RepositoryAnnotator> requestedAnnotatorList, Repository<Entity> repo, EntityTypeFactory entityTypeFactory)
Queue<RepositoryAnnotator>	AnnotatorDependencyOrderResolver.getAnnotatorSelectionDependencyList(List<RepositoryAnnotator> availableAnnotatorList, List<RepositoryAnnotator> requestedAnnotatorList, Repository<Entity> repo, EntityTypeFactory entityTypeFactory)

Uses of RepositoryAnnotator in org.molgenis.data.annotation.web

Methods in org.molgenis.data.annotation.web that return RepositoryAnnotator

Modifier and Type	Method and Description
RepositoryAnnotator	AnnotationServiceImpl.getAnnotatorByName(String annotatorName)
RepositoryAnnotator	AnnotationService.getAnnotatorByName(String annotatorName)

Methods in org.molgenis.data.annotation.web that return types with arguments of type RepositoryAnnotator

Modifier and Type	Method and Description
List<RepositoryAnnotator>	AnnotationServiceImpl.getAllAnnotators()
List<RepositoryAnnotator>	AnnotationService.getAllAnnotators()
List<RepositoryAnnotator>	AnnotationServiceImpl.getAnnotatorsByMetaData(EntityType metaData)
List<RepositoryAnnotator>	AnnotationService.getAnnotatorsByMetaData(EntityType metaData)

Methods in org.molgenis.data.annotation.web with parameters of type RepositoryAnnotator

Modifier and Type	Method and Description
void	CrudRepositoryAnnotator.annotate(RepositoryAnnotator annotator, Repository<Entity> repository)