Index (data-annotators 5.1.0 API)

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

A

AbstractAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.framework: The most standard implementation of an EntityAnnotator that first creates a query, queries the resource, then filters the results using a ResultFilter and then copies the resulting attributes to the annotated Entity.
AbstractAnnotator(String, AnnotatorInfo, QueryCreator, ResultFilter, DataService, Resources, CmdLineAnnotatorSettingsConfigurer) - Constructor for class org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator
AbstractRepositoryAnnotator - Class in org.molgenis.data.annotation.core
AbstractRepositoryAnnotator() - Constructor for class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator
AbstractRepositoryEntityAnnotator - Class in org.molgenis.data.annotation.core
AbstractRepositoryEntityAnnotator() - Constructor for class org.molgenis.data.annotation.core.AbstractRepositoryEntityAnnotator
addAnnotatorMetaDataToRepositories(EntityType, AttributeFactory, RepositoryAnnotator) - Static method in class org.molgenis.data.annotation.core.utils.AnnotatorUtils: Adds a new compound attribute to an existing CrudRepository
addSettings(String) - Method in interface org.molgenis.data.annotation.core.resources.CmdLineAnnotatorSettingsConfigurer
addSettings(String) - Method in class org.molgenis.data.annotation.web.settings.SingleFileLocationCmdLineAnnotatorSettingsConfigurer
AGE_GROUP_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
ALT - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
ANN - Static variable in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
annotate(Iterator<Entity>) - Method in class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator
annotate(Iterable<Entity>) - Method in class org.molgenis.data.annotation.core.AbstractRepositoryEntityAnnotator
annotate(Iterable<Entity>, boolean) - Method in class org.molgenis.data.annotation.core.AbstractRepositoryEntityAnnotator
annotate(Iterable<Entity>) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
annotate(Iterable<Entity>, boolean) - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
annotate(Iterable<Entity>) - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
annotate(Iterator<Entity>) - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
annotate(RepositoryAnnotator, VcfAttributes, EntityTypeFactory, AttributeFactory, EffectStructureConverter, File, File, List<String>, boolean) - Static method in class org.molgenis.data.annotation.core.utils.CmdLineAnnotatorUtils: Adds a new compound attribute to an existing CrudRepository
annotate(RepositoryAnnotator, Repository<Entity>) - Method in class org.molgenis.data.annotation.web.CrudRepositoryAnnotator
annotateEntity(Entity, boolean) - Method in class org.molgenis.data.annotation.core.AbstractRepositoryEntityAnnotator
annotateEntity(Entity, boolean) - Method in interface org.molgenis.data.annotation.core.entity.EntityAnnotator: Annotates a single entity.
annotateEntity(Entity, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
annotateEntity(Entity, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
ANNOTATION - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
ANNOTATION_JOB_EXECUTION - Static variable in class org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData
annotationDataExists() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
annotationDataExists() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
annotationDataExists() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator: Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
AnnotationException - Exception in org.molgenis.data.annotation.core.exception
AnnotationException(Entity, int, List<Attribute>, String, Throwable) - Constructor for exception org.molgenis.data.annotation.core.exception.AnnotationException
AnnotationException(AnnotationException) - Constructor for exception org.molgenis.data.annotation.core.exception.AnnotationException
AnnotationJobExecution - Class in org.molgenis.data.annotation.web.meta
AnnotationJobExecution(Entity) - Constructor for class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
AnnotationJobExecution(EntityType) - Constructor for class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
AnnotationJobExecution(String, EntityType) - Constructor for class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
AnnotationJobExecutionFactory - Class in org.molgenis.data.annotation.web.meta
AnnotationJobExecutionMetaData - Class in org.molgenis.data.annotation.web.meta
AnnotationService - Interface in org.molgenis.data.annotation.web: Created with IntelliJ IDEA.
AnnotationServiceImpl - Class in org.molgenis.data.annotation.web
AnnotationServiceImpl() - Constructor for class org.molgenis.data.annotation.web.AnnotationServiceImpl
Annotator - Interface in org.molgenis.data.annotation.core.entity: An Annotator.
ANNOTATOR_PREFIX - Static variable in interface org.molgenis.data.annotation.core.RepositoryAnnotator
AnnotatorBootstrapper - Class in org.molgenis.data.annotation.web.bootstrap
AnnotatorBootstrapper() - Constructor for class org.molgenis.data.annotation.web.bootstrap.AnnotatorBootstrapper
AnnotatorConfig - Interface in org.molgenis.data.annotation.core.entity
AnnotatorDependencyOrderResolver - Class in org.molgenis.data.annotation.core.utils
AnnotatorDependencyOrderResolver() - Constructor for class org.molgenis.data.annotation.core.utils.AnnotatorDependencyOrderResolver
AnnotatorEntityType - Interface in org.molgenis.data.annotation.web.meta
AnnotatorInfo - Class in org.molgenis.data.annotation.core.entity: Informatin about an Annotator
AnnotatorInfo() - Constructor for class org.molgenis.data.annotation.core.entity.AnnotatorInfo
AnnotatorInfo.Status - Enum in org.molgenis.data.annotation.core.entity
AnnotatorInfo.Type - Enum in org.molgenis.data.annotation.core.entity
ANNOTATORS - Static variable in class org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData
AnnotatorUtils - Class in org.molgenis.data.annotation.core.utils
AnnotatorUtils() - Constructor for class org.molgenis.data.annotation.core.utils.AnnotatorUtils
AttributeEqualsQueryCreator - Class in org.molgenis.data.annotation.core.query: Create a query that finds rows that match gene name
AttributeEqualsQueryCreator(Attribute) - Constructor for class org.molgenis.data.annotation.core.query.AttributeEqualsQueryCreator

B

blockCompressedInputStream - Variable in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
bootstrap(ContextRefreshedEvent) - Method in class org.molgenis.data.annotation.web.bootstrap.AnnotatorBootstrapper

C

C_DNA_POSITION - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
cadd() - Method in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CADD_ABS - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CADD_ABS_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CADD_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings.Meta
CADD_SCALED - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CADD_SCALED_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CADD_TABIX_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CaddAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
CaddAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
CaddAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
CaddAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings
CaddAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
canAnnotate(EntityType) - Method in class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator
canAnnotate(EntityType) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
canAnnotate(EntityType) - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator: Returns null if the annotator will work for the given metadata, a reason if not so
Category - Enum in org.molgenis.data.annotation.core.entity.impl.gavin
CDS_POSITION - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
cgd() - Method in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
CGD_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings.Meta
CGDAnnotator - Class in org.molgenis.data.annotation.core.entity.impl: Annotator that can add HGNC_ID and ENTREZ_GENE_ID and other attributes to an EntityType that has a attribute named 'GENE' that must be the HGNC gene dataType.
CGDAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
CGDAnnotator.CGDAttributeName - Enum in org.molgenis.data.annotation.core.entity.impl
CGDAnnotator.GeneralizedInheritance - Enum in org.molgenis.data.annotation.core.entity.impl
CGDAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
CGDAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings
CGDAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
cgdResource() - Method in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
CHROMOSOMES - Static variable in class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
CHROMOSOMES - Static variable in class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
CLASSIFICATION - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
classifyVariant(Impact, Double, Double, String, GavinThresholds) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm: Classifies a variant using the given GavinThresholds.
clinvar() - Method in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLINALL_ResourceAttributeName - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLNALLE - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLNALLE_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLNSIG - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLNSIG_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_CLNSIG_ResourceAttributeName - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
CLINVAR_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings.Meta
CLINVAR_TABIX_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
ClinvarAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
ClinvarAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
ClinvarAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
ClinvarAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings
ClinvarAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
ClinvarMultiAllelicResultFilter - Class in org.molgenis.data.annotation.core.filter
ClinvarMultiAllelicResultFilter(VcfAttributes) - Constructor for class org.molgenis.data.annotation.core.filter.ClinvarMultiAllelicResultFilter
CmdLineAnnotatorSettingsConfigurer - Interface in org.molgenis.data.annotation.core.resources: Each annotator must supply a concrete instance of this interface to configure the MolgenisSettings for the CmdLineAnnotator
CmdLineAnnotatorUtils - Class in org.molgenis.data.annotation.core.utils
CmdLineAnnotatorUtils() - Constructor for class org.molgenis.data.annotation.core.utils.CmdLineAnnotatorUtils
CONDITION_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
CONFIDENCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
count() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
count() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
create(Entity) - Static method in class org.molgenis.data.annotation.core.datastructures.Location
create(AnnotatorInfo.Status, AnnotatorInfo.Type, String, String, List<Attribute>) - Static method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
create(Double, Double, Double, Double, Double, Category) - Static method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
create(Judgment.Classification, Judgment.Method, String, String) - Static method in class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
createAnnotatorAttributes(AttributeFactory) - Method in interface org.molgenis.data.annotation.core.entity.Annotator: Use this method for the actual annotation process, to ensure that unique identifiers by creating a new set of attributes everytime an annotator us executed
createAnnotatorAttributes(AttributeFactory) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
createAnnotatorAttributes(AttributeFactory) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
createAnnotatorAttributes(AttributeFactory) - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
createCaddScaledAttr(AttributeFactory) - Static method in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
createExacOutputAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
createQuery(Entity) - Method in interface org.molgenis.data.annotation.core.entity.QueryCreator
createQuery(Entity) - Method in class org.molgenis.data.annotation.core.query.AttributeEqualsQueryCreator
createQuery(Entity) - Method in class org.molgenis.data.annotation.core.query.GeneNameQueryCreator
createQuery(Entity) - Method in class org.molgenis.data.annotation.core.query.LocusQueryCreator
createQuery(Locus) - Static method in class org.molgenis.data.annotation.core.query.LocusQueryCreator
createRepository(File) - Method in class org.molgenis.data.annotation.core.resources.impl.emx.InMemoryRepositoryFactory
createRepository(File) - Method in interface org.molgenis.data.annotation.core.resources.impl.RepositoryFactory
createRepository(File) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepositoryFactory
createRepository(File) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepositoryFactory
createVariantEffectStructure(String, List<Attribute>, VcfRepository) - Method in class org.molgenis.data.annotation.core.utils.EffectStructureConverter
createVcfEntityStructure(Iterator<Entity>) - Method in class org.molgenis.data.annotation.core.utils.EffectStructureConverter
CrudRepositoryAnnotator - Class in org.molgenis.data.annotation.web
CrudRepositoryAnnotator(DataService, PermissionSystemService, AttributeFactory) - Constructor for class org.molgenis.data.annotation.web.CrudRepositoryAnnotator

D

dann() - Method in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
DANN_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.DannAnnotatorSettings.Meta
DANN_SCORE - Static variable in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
DANN_SCORE_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
DANN_TABIX_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
DannAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
DannAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
DannAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
DannAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.DannAnnotatorSettings
DannAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
DEFAULT_CHROMOSOMES - Static variable in class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl
DEFAULT_PATTERN - Static variable in class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl
DEFAULT_ROOT_DIRECTORY - Static variable in class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl
DISTANCE_TO_FEATURE - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData

E

EffectBasedAnnotator - Class in org.molgenis.data.annotation.core: Annotator that annotates the "effects" entities rather than the variants themself
EffectBasedAnnotator(String) - Constructor for class org.molgenis.data.annotation.core.EffectBasedAnnotator
EffectCreatingAnnotator - Interface in org.molgenis.data.annotation.core: Annotator that annotates variant but instead of adding columns to the variant it creates new "effects" entities with an xref to the variant.
EffectsMetaData - Class in org.molgenis.data.annotation.core.effects
EffectsMetaData() - Constructor for class org.molgenis.data.annotation.core.effects.EffectsMetaData
EffectStructureConverter - Class in org.molgenis.data.annotation.core.utils: This class is used to convert from (MOLGENIS)SnpEff annotated VCF files to the entity structure expected by Effects annotators (for example GAVIN), and the other way around
EffectStructureConverter(EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.utils.EffectStructureConverter
EmxResourceImpl - Class in org.molgenis.data.annotation.core.resources.impl.emx
EmxResourceImpl(String, SingleResourceConfig) - Constructor for class org.molgenis.data.annotation.core.resources.impl.emx.EmxResourceImpl
ENTITY_NAME_SUFFIX - Static variable in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
EntityAnnotator - Interface in org.molgenis.data.annotation.core.entity: Simple interface to implement for fine-grained annotators.
EntityProcessor - Interface in org.molgenis.data.annotation.core.entity: A step to use in the Annotator.
equals(Object) - Method in class org.molgenis.data.annotation.core.datastructures.Locus
ERRORS - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
exac() - Method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HET - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HET_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HET_ResourceAttributeName - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HOM - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HOM_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AC_HOM_ResourceAttributeName - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AF - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AF_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_AF_ResourceAttributeName - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
EXAC_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings.Meta
EXAC_TABIX_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
ExacAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
ExacAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
ExacAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
ExacAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings
ExacAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
EXTRA_SENSITIVITY_FACTOR - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm: Sensitivity is more important than specificity, so we can adjust this parameter to globally adjust the thresholds.

F

FEATURE_ID - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
FEATURE_TYPE - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
filename - Variable in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
FILEPATTERN - Static variable in class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
FILEPATTERN - Static variable in class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
filterResults(Iterable<Entity>, Entity, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HpoResultFilter
filterResults(Iterable<Entity>, Entity, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimResultFilter
filterResults(Iterable<Entity>, Entity, boolean) - Method in interface org.molgenis.data.annotation.core.entity.ResultFilter
filterResults(Iterable<Entity>, Entity, boolean) - Method in class org.molgenis.data.annotation.core.filter.ClinvarMultiAllelicResultFilter
filterResults(Iterable<Entity>, Entity, boolean) - Method in class org.molgenis.data.annotation.core.filter.FirstResultFilter
filterResults(Iterable<Entity>, Entity, boolean) - Method in class org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.MultiFileResource
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.ResourceImpl: Searches the repository if it is available.
findAll(String, Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.ResourcesImpl
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
findAll(Query<Entity>) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository
findAll(Query<Entity>) - Method in interface org.molgenis.data.annotation.core.resources.Resource: Queries this Resource
findAll(String, Query<Entity>) - Method in interface org.molgenis.data.annotation.core.resources.Resources: Queries a resource.
FirstResultFilter - Class in org.molgenis.data.annotation.core.filter: ResultFilter that just returns the first result
FirstResultFilter() - Constructor for class org.molgenis.data.annotation.core.filter.FirstResultFilter
fitcon() - Method in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
FITCON_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings.Meta
FITCON_SCORE - Static variable in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
FITCON_SCORE_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
FITCON_TABIX_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
FitConAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
FitConAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
FitConAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
FitConAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings
FitConAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
fromEntity(Entity) - Static method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds

G

gavin() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
GavinAlgorithm - Class in org.molgenis.data.annotation.core.entity.impl.gavin
GavinAlgorithm() - Constructor for class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm
GavinAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.gavin
GavinAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
GavinAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
GavinAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings
GavinAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
GavinThresholds - Class in org.molgenis.data.annotation.core.entity.impl.gavin
GavinThresholds() - Constructor for class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
GENE_ID - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
GENE_NAME - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
GeneCsvRepository - Class in org.molgenis.data.annotation.core.resources.impl
GeneCsvRepository(File, String, String, EntityTypeFactory, AttributeFactory, char) - Constructor for class org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
GeneNameQueryCreator - Class in org.molgenis.data.annotation.core.query
GeneNameQueryCreator() - Constructor for class org.molgenis.data.annotation.core.query.GeneNameQueryCreator
GENERALIZED_INHERITANCE_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
GENOMEWIDE_CADD_THRESHOLD - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm
GENOMEWIDE_MAF_THRESHOLD - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm
genomewideClassifyVariant(Impact, Double, Double, String) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm: Classifies a variant based on genome-wide thresholds
getAllAnnotators() - Method in interface org.molgenis.data.annotation.web.AnnotationService
getAllAnnotators() - Method in class org.molgenis.data.annotation.web.AnnotationServiceImpl
getAltAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getAnnotationAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getAnnotatorAttributes() - Method in interface org.molgenis.data.annotation.core.entity.Annotator: Be aware that several calls to this function will give you the same auto identifiers every time
getAnnotatorAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
getAnnotatorByName(String) - Method in interface org.molgenis.data.annotation.web.AnnotationService
getAnnotatorByName(String) - Method in class org.molgenis.data.annotation.web.AnnotationServiceImpl
getAnnotatorName() - Method in exception org.molgenis.data.annotation.core.exception.AnnotationException
getAnnotatorResourceDir() - Static method in class org.molgenis.data.annotation.core.utils.AnnotatorUtils
getAnnotators() - Method in class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
getAnnotatorsByMetaData(EntityType) - Method in interface org.molgenis.data.annotation.web.AnnotationService
getAnnotatorsByMetaData(EntityType) - Method in class org.molgenis.data.annotation.web.AnnotationServiceImpl
getAnnotatorSelectionDependencyList(List<RepositoryAnnotator>, List<RepositoryAnnotator>, Repository<Entity>, EntityTypeFactory) - Method in class org.molgenis.data.annotation.core.utils.AnnotatorDependencyOrderResolver
getAttributeName() - Method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName
getCapabilities() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
getCapabilities() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
getCapabilities() - Method in class org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
getCapabilities() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
getCapabilities() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository
getCategory() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getCdnaPositionAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getCdsPositionAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getCgdName(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName
getCgdName() - Method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName
getChrom() - Method in class org.molgenis.data.annotation.core.datastructures.Location
getChrom() - Method in class org.molgenis.data.annotation.core.datastructures.Locus
getClassification() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
getCmdLineAnnotatorSettingsConfigurer() - Method in interface org.molgenis.data.annotation.core.entity.EntityAnnotator
getCmdLineAnnotatorSettingsConfigurer() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
getCmdLineAnnotatorSettingsConfigurer() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
getCmdLineAnnotatorSettingsConfigurer() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getCmdLineAnnotatorSettingsConfigurer() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
getCode() - Method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
getConfidence() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
getConfigs() - Method in class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl
getConfigs() - Method in interface org.molgenis.data.annotation.core.resources.MultiResourceConfig
getCsvParser() - Static method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
getDescription() - Method in class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator
getDescription() - Method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
getDescription() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
getDistanceToFeatureAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getEffectDescription(Attribute) - Method in class org.molgenis.data.annotation.core.utils.EffectStructureConverter
getEntityNumber() - Method in exception org.molgenis.data.annotation.core.exception.AnnotationException
getEntityType() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
getEntityType() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
getEntityType() - Method in class org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
getEntityType() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
getEntryAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
getErrorsAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getExacAcHetAttr(AttributeFactory) - Static method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
getExacAcHomAttr(AttributeFactory) - Static method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
getExacAFAttr(AttributeFactory) - Static method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
getFailedEntity() - Method in exception org.molgenis.data.annotation.core.exception.AnnotationException
getFeatureIdAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getFeatureTypeAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getFile() - Method in class org.molgenis.data.annotation.core.resources.impl.SingleResourceConfig
getFile() - Method in interface org.molgenis.data.annotation.core.resources.ResourceConfig
getFullName() - Method in class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator
getFullName() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
getGene() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
getGeneIdAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getGeneNameAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getHgvsCAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getHgvsPAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getIdsAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
getInfo() - Method in interface org.molgenis.data.annotation.core.entity.Annotator
getInfo() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
getInfo() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
getInfo() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getInfo() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator
getInputVcfFile(Iterator<Entity>) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner: Converts entities to a VCF file that can be passed to SnpEff.
getLines(TabixReader.Iterator) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository: Collect the lines returned in a TabixReader.Iterator.
getMeanPathogenicCADDScore() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getMeanPopulationCADDScore() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getMessage() - Method in exception org.molgenis.data.annotation.core.exception.UiAnnotationException
getMimNumberAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
getName() - Method in class org.molgenis.data.annotation.core.resources.impl.MultiFileResource
getName() - Method in class org.molgenis.data.annotation.core.resources.impl.ResourceImpl
getName() - Method in interface org.molgenis.data.annotation.core.resources.Resource
getOmimLocationAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
getOrderedAttributes() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getOrderedAttributes() - Method in interface org.molgenis.data.annotation.web.meta.AnnotatorEntityType
getOutputAttributes() - Method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
getOutputAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
getOutputAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getOutputAttributes() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator: returns an EntityType containing the attributes the annotator will add
getPathoMAFThreshold() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getPhenotypeAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
getPos() - Method in class org.molgenis.data.annotation.core.datastructures.Location
getPos() - Method in class org.molgenis.data.annotation.core.datastructures.Locus
getProteinPositionAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getPutativeImpactAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getRankTotalAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getReason() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
getRepositoryFactory() - Method in interface org.molgenis.data.annotation.core.resources.Resource
getRequiredAttributes() - Method in interface org.molgenis.data.annotation.core.entity.EntityAnnotator
getRequiredAttributes() - Method in interface org.molgenis.data.annotation.core.entity.EntityProcessor
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HpoResultFilter
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimResultFilter
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getRequiredAttributes() - Method in exception org.molgenis.data.annotation.core.exception.AnnotationException
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.filter.ClinvarMultiAllelicResultFilter
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.filter.FirstResultFilter
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.query.AttributeEqualsQueryCreator
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.query.GeneNameQueryCreator
getRequiredAttributes() - Method in class org.molgenis.data.annotation.core.query.LocusQueryCreator
getRequiredAttributes() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator: Returns a EntityType containing the attributes needed for the annotator to work
getResourceAttributeValue(Attribute, Entity) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator: Get the resource attribute value for one of this annotator's output attributes.
getResourcesNames() - Method in class org.molgenis.data.annotation.core.resources.impl.ResourcesImpl
getResourcesNames() - Method in interface org.molgenis.data.annotation.core.resources.Resources
getSens95thPerCADDThreshold() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getSimpleName() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
getSimpleName() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getSimpleName() - Method in interface org.molgenis.data.annotation.core.RepositoryAnnotator: Return the name of the annotator
getSnpEffects(Iterable<Entity>) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
getSnpEffects(Iterator<Entity>, File) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
getSnpEffPath() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner: Gets the path to the SnpEff JAR.
getSpec95thPerCADDThreshold() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
getStatus() - Method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
getTargetEntityType(EntityType) - Method in interface org.molgenis.data.annotation.core.EffectCreatingAnnotator: Annotators that add a new repository need the source meta data to construct the new repository's meta data.
getTargetEntityType(EntityType) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
getTargetEntityType(EntityType) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
getTargetName() - Method in class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
getTermsAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
getTranscriptBiotypeAttr() - Method in class org.molgenis.data.annotation.core.effects.EffectsMetaData
getType() - Method in class org.molgenis.data.annotation.core.entity.AnnotatorInfo
getTypeAttr() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
gonl() - Method in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GONL_AF_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GONL_GENOME_AF - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GONL_GENOME_GTC - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GONL_GTC_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GONL_MULTI_FILE_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GoNLAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
GoNLAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
GoNLAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
GoNLAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings
GoNLAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings

H

hashCode() - Method in class org.molgenis.data.annotation.core.datastructures.Locus
hasRepository(String) - Method in class org.molgenis.data.annotation.core.resources.impl.ResourcesImpl
hasRepository(String) - Method in interface org.molgenis.data.annotation.core.resources.Resources: Indicates if a specific Resource is currently available.
HGVS_C - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
HGVS_P - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
hpo() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
HPO_DISEASE_ID_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
HPO_GENE_SYMBOL_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
HPO_ID_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
HPO_IDS - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
HPO_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings.Meta
HPO_TERM_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
HPO_TERMS - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
HPOAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.hpo: Typical HPO terms for a gene dataType (already present via SnpEff) Source: http://compbio.charite.de/hudson/job/hpo.
HPOAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
HPOAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
HPOAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings
HPOAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
HPORepository - Class in org.molgenis.data.annotation.core.entity.impl.hpo
HPORepository(File, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
hpoResource() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
HpoResultFilter - Class in org.molgenis.data.annotation.core.entity.impl.hpo
HpoResultFilter(EntityTypeFactory, AttributeFactory, HPOAnnotator) - Constructor for class org.molgenis.data.annotation.core.entity.impl.hpo.HpoResultFilter

I

ID - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
ID - Static variable in class org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings
ID - Static variable in class org.molgenis.data.annotation.web.settings.DannAnnotatorSettings
ID - Static variable in class org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings
ID - Static variable in class org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings
Impact - Enum in org.molgenis.data.annotation.core.entity.impl.snpeff
INFO_AC - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
INFO_AN - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
INFO_GTC - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
INHERITANCE_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
init(EntityAnnotator) - Method in class org.molgenis.data.annotation.core.EffectBasedAnnotator
init() - Method in interface org.molgenis.data.annotation.core.entity.AnnotatorConfig
init() - Method in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
init(EntityAnnotator) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
init() - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator
init(SnpEffRunner, Entity, VcfAttributes, EffectsMetaData, DataService) - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
init() - Method in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
init() - Method in class org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData
init() - Method in class org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.DannAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings.Meta
init() - Method in class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
InMemoryRepositoryFactory - Class in org.molgenis.data.annotation.core.resources.impl.emx: Factory that can instantiate a InMemoryRepository.
InMemoryRepositoryFactory(String, String, MetaDataParser, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.resources.impl.emx.InMemoryRepositoryFactory
isAboveMeanPathogenicCADDScore(double) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
isAbovePathoMAFThreshold(Double) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
isAboveSpec95thPerCADDThreshold(double) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
isAvailable() - Method in class org.molgenis.data.annotation.core.resources.impl.emx.EmxResourceImpl
isAvailable() - Method in class org.molgenis.data.annotation.core.resources.impl.MultiFileResource
isAvailable() - Method in class org.molgenis.data.annotation.core.resources.impl.ResourceImpl: Indicates if the resource is available.
isAvailable() - Method in interface org.molgenis.data.annotation.core.resources.Resource
isBelowMeanPopulationCADDScore(double) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
isBelowSens95PerCADDThreshold(double) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
iterator() - Method in class org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
iterator() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
iterator() - Method in class org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
Iterator(int, int, int, TabixReader.TPair64[]) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader.Iterator
iterator() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository

J

JarRunner - Interface in org.molgenis.data.annotation.core.utils: Created by charbonb on 24/08/15.
JarRunnerImpl - Class in org.molgenis.data.annotation.core.utils
JarRunnerImpl() - Constructor for class org.molgenis.data.annotation.core.utils.JarRunnerImpl
JsonReader - Class in org.molgenis.data.annotation.core.utils
JsonReader() - Constructor for class org.molgenis.data.annotation.core.utils.JsonReader
Judgment - Class in org.molgenis.data.annotation.core.entity.impl.gavin: Judgment result of the gavin method
Judgment() - Constructor for class org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
Judgment.Classification - Enum in org.molgenis.data.annotation.core.entity.impl.gavin
Judgment.Method - Enum in org.molgenis.data.annotation.core.entity.impl.gavin

L

Location - Class in org.molgenis.data.annotation.core.datastructures: Used to compare equality of Chrom/Pos values in the MultiAllelicResultFilter.
Location() - Constructor for class org.molgenis.data.annotation.core.datastructures.Location
Locus - Class in org.molgenis.data.annotation.core.datastructures: Created by jvelde on 2/13/14.
Locus(String, Integer) - Constructor for class org.molgenis.data.annotation.core.datastructures.Locus
LocusQueryCreator - Class in org.molgenis.data.annotation.core.query: Creates a Locus query that finds rows that match chromosome/position
LocusQueryCreator(VcfAttributes) - Constructor for class org.molgenis.data.annotation.core.query.LocusQueryCreator

M

main(String[]) - Static method in class org.molgenis.data.annotation.core.utils.JsonReader
mChr2tid - Variable in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
MEAN_PATHOGENIC_CADD_SCORE - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
MEAN_POPULATION_CADD_SCORE - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
merge(Iterable<Entity>) - Method in class org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter: Combine ALT information per reference allele (in VCF there is only 1 reference by letting ALT vary, but that might not always be the case)
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.DannAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings.Meta
Meta() - Constructor for class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
MultiAllelicResultFilter - Class in org.molgenis.data.annotation.core.filter: TODO: Support multi-allelic combination fields.
MultiAllelicResultFilter(List<Attribute>, boolean, VcfAttributes) - Constructor for class org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter
MultiAllelicResultFilter(List<Attribute>, VcfAttributes) - Constructor for class org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter
MultiFileResource - Class in org.molgenis.data.annotation.core.resources.impl
MultiFileResource(String, MultiResourceConfig) - Constructor for class org.molgenis.data.annotation.core.resources.impl.MultiFileResource
MultiResourceConfig - Interface in org.molgenis.data.annotation.core.resources: Created by charbonb on 15/06/15.
MultiResourceConfigImpl - Class in org.molgenis.data.annotation.core.resources.impl: Created by charbonb on 15/06/15.
MultiResourceConfigImpl(String, String, String, String, Entity) - Constructor for class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl: overrideChromosomeFiles contains the chromosome that do not comply with the pattern.
MultiResourceConfigImpl(String, String, String, Entity) - Constructor for class org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl

N

NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.CaddAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.CGDAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.DannAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.ExacAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.FitConAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
next() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader.Iterator

O

omim() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_AUTO_ID_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_CAUSAL_IDENTIFIER - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_CYTO_LOCATION_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_CYTO_LOCATIONS - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_DISORDER - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_ENTRY - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_ENTRY_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_GENE_SYMBOLS_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings.Meta
OMIM_MIM_NUMBER_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_PHENOTYPE_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OMIM_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_TYPE - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OMIM_TYPE_COL_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
OmimAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.omim
OmimAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OmimAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
OmimAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings
OmimAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
OmimRepository - Class in org.molgenis.data.annotation.core.entity.impl.omim
OmimRepository(File, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
omimResource() - Method in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
OmimResultFilter - Class in org.molgenis.data.annotation.core.entity.impl.omim
OmimResultFilter(EntityTypeFactory, AttributeFactory, OmimAnnotator) - Constructor for class org.molgenis.data.annotation.core.entity.impl.omim.OmimResultFilter
org.molgenis.data.annotation.core - package org.molgenis.data.annotation.core
org.molgenis.data.annotation.core.datastructures - package org.molgenis.data.annotation.core.datastructures
org.molgenis.data.annotation.core.effects - package org.molgenis.data.annotation.core.effects
org.molgenis.data.annotation.core.entity - package org.molgenis.data.annotation.core.entity
org.molgenis.data.annotation.core.entity.impl - package org.molgenis.data.annotation.core.entity.impl
org.molgenis.data.annotation.core.entity.impl.framework - package org.molgenis.data.annotation.core.entity.impl.framework
org.molgenis.data.annotation.core.entity.impl.gavin - package org.molgenis.data.annotation.core.entity.impl.gavin
org.molgenis.data.annotation.core.entity.impl.hpo - package org.molgenis.data.annotation.core.entity.impl.hpo
org.molgenis.data.annotation.core.entity.impl.omim - package org.molgenis.data.annotation.core.entity.impl.omim
org.molgenis.data.annotation.core.entity.impl.snpeff - package org.molgenis.data.annotation.core.entity.impl.snpeff
org.molgenis.data.annotation.core.exception - package org.molgenis.data.annotation.core.exception
org.molgenis.data.annotation.core.filter - package org.molgenis.data.annotation.core.filter
org.molgenis.data.annotation.core.query - package org.molgenis.data.annotation.core.query
org.molgenis.data.annotation.core.resources - package org.molgenis.data.annotation.core.resources
org.molgenis.data.annotation.core.resources.impl - package org.molgenis.data.annotation.core.resources.impl
org.molgenis.data.annotation.core.resources.impl.emx - package org.molgenis.data.annotation.core.resources.impl.emx
org.molgenis.data.annotation.core.resources.impl.tabix - package org.molgenis.data.annotation.core.resources.impl.tabix
org.molgenis.data.annotation.core.utils - package org.molgenis.data.annotation.core.utils
org.molgenis.data.annotation.web - package org.molgenis.data.annotation.web
org.molgenis.data.annotation.web.bootstrap - package org.molgenis.data.annotation.web.bootstrap
org.molgenis.data.annotation.web.meta - package org.molgenis.data.annotation.web.meta
org.molgenis.data.annotation.web.settings - package org.molgenis.data.annotation.web.settings
OVERRIDE_CHROMOSOME_FILES - Static variable in class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
OVERRIDE_CHROMOSOME_FILES - Static variable in class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta

P

PATHO_MAF_THRESHOLD - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
processQueryResults(Entity, Iterable<Entity>, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator
processQueryResults(Entity, Iterable<Entity>, boolean) - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl: Processes the query results.
PROTEIN_POSITION - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
PUTATIVE_IMPACT - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData

Q

query(int, int, int) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
query(String) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
query(String, int, int) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository: Queries the tabix reader.
QueryAnnotatorImpl - Class in org.molgenis.data.annotation.core.entity.impl.framework: Base class for any EntityAnnotator that uses a QueryCreator to query the DataService or Resources.
QueryAnnotatorImpl(String, AnnotatorInfo, QueryCreator, DataService, Resources, CmdLineAnnotatorSettingsConfigurer) - Constructor for class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
QueryCreator - Interface in org.molgenis.data.annotation.core.entity: Creates a query to send to the annotator's source repository to find rows to annotate with.

R

RANK_TOTAL - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
readIndex(File) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader: Read the Tabix index from a file
readIndex(String) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader: Read the Tabix index from the default file.
readInt(InputStream) - Static method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
readJsonFromUrl(String) - Static method in class org.molgenis.data.annotation.core.utils.JsonReader
readLine(InputStream) - Static method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
readLine() - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader: Read one line from the data file.
readLong(InputStream) - Static method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
REASON - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
RepositoryAnnotator - Interface in org.molgenis.data.annotation.core: interface for annotators.
RepositoryAnnotatorImpl - Class in org.molgenis.data.annotation.core.entity.impl.framework
RepositoryAnnotatorImpl(String) - Constructor for class org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
RepositoryFactory - Interface in org.molgenis.data.annotation.core.resources.impl
RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
Resource - Interface in org.molgenis.data.annotation.core.resources: A Resource that can be queried and that may be unavailable.
RESOURCE_ENTITY_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator
ResourceConfig - Interface in org.molgenis.data.annotation.core.resources: Created by charbonb on 15/06/15.
ResourceImpl - Class in org.molgenis.data.annotation.core.resources.impl: Implementation of Resource, a file-based repository.
ResourceImpl(String, ResourceConfig) - Constructor for class org.molgenis.data.annotation.core.resources.impl.ResourceImpl: Creates a new Resource
Resources - Interface in org.molgenis.data.annotation.core.resources
ResourcesImpl - Class in org.molgenis.data.annotation.core.resources.impl
ResourcesImpl() - Constructor for class org.molgenis.data.annotation.core.resources.impl.ResourcesImpl
ResultFilter - Interface in org.molgenis.data.annotation.core.entity
ROOT_DIRECTORY - Static variable in class org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
ROOT_DIRECTORY - Static variable in class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
runJar(String, List<String>, File) - Method in interface org.molgenis.data.annotation.core.utils.JarRunner
runJar(String, List<String>, File) - Method in class org.molgenis.data.annotation.core.utils.JarRunnerImpl

S

SENS_95TH_PER_CADD_THRESHOLD - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
SEPARATOR - Static variable in class org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator
setAnnotators(String) - Method in class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
setTargetName(String) - Method in class org.molgenis.data.annotation.web.meta.AnnotationJobExecution
SingleFileLocationCmdLineAnnotatorSettingsConfigurer - Class in org.molgenis.data.annotation.web.settings: CmdLineAnnotatorSettingsConfigurer that defines a single property
SingleFileLocationCmdLineAnnotatorSettingsConfigurer(String, Entity) - Constructor for class org.molgenis.data.annotation.web.settings.SingleFileLocationCmdLineAnnotatorSettingsConfigurer
SingleResourceConfig - Class in org.molgenis.data.annotation.core.resources.impl
SingleResourceConfig(String, Entity) - Constructor for class org.molgenis.data.annotation.core.resources.impl.SingleResourceConfig
snpEff() - Method in class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator
SNPEFF_JAR_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings.Meta
SnpEffAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.snpeff: SnpEff annotator
SnpEffAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator
SnpEffAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
SnpEffAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings
SnpEffAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
SnpEffRepositoryAnnotator - Class in org.molgenis.data.annotation.core.entity.impl.snpeff
SnpEffRepositoryAnnotator(String) - Constructor for class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator
SnpEffRunner - Class in org.molgenis.data.annotation.core.entity.impl.snpeff
SnpEffRunner(JarRunner, Entity, IdGenerator, VcfAttributes, EffectsMetaData, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
sourceExists() - Method in interface org.molgenis.data.annotation.core.entity.EntityAnnotator
sourceExists() - Method in class org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl
SPEC_95TH_PER_CADD_THRESHOLD - Static variable in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds

T

TabixReader - Class in org.molgenis.data.annotation.core.resources.impl.tabix
TabixReader(String) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader: The constructor
TabixReader.Iterator - Class in org.molgenis.data.annotation.core.resources.impl.tabix
TabixRepository - Class in org.molgenis.data.annotation.core.resources.impl.tabix
TabixRepository(File, EntityType) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository: Creates a new TabixRepository
TabixRepository(File, EntityType, String, String) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
TabixRepositoryFactory - Class in org.molgenis.data.annotation.core.resources.impl.tabix: Factory that can instantiate a TabixRepository.
TabixRepositoryFactory(EntityType) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepositoryFactory
TabixVcfRepository - Class in org.molgenis.data.annotation.core.resources.impl.tabix: An indexed VCF Repository
TabixVcfRepository(File, String, VcfAttributes, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository
TabixVcfRepositoryFactory - Class in org.molgenis.data.annotation.core.resources.impl.tabix: Factory that can create a TabixVcfRepository.
TabixVcfRepositoryFactory(String, VcfAttributes, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepositoryFactory
TARGET_NAME - Static variable in class org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData
THOUSAND_GENOME_AF - Static variable in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
THOUSAND_GENOME_AF_LABEL - Static variable in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
THOUSAND_GENOME_AF_RESOURCE_ATTRIBUTE_NAME - Static variable in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
THOUSAND_GENOME_MULTI_FILE_RESOURCE - Static variable in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
thousandGenomes() - Method in class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
ThousandGenomesAnnotator - Class in org.molgenis.data.annotation.core.entity.impl
ThousandGenomesAnnotator() - Constructor for class org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator
ThousendGenomesAnnotatorSettings - Class in org.molgenis.data.annotation.web.settings
ThousendGenomesAnnotatorSettings() - Constructor for class org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings
ThousendGenomesAnnotatorSettings.Meta - Class in org.molgenis.data.annotation.web.settings
toAlleleMap(String, String) - Static method in class org.molgenis.data.annotation.core.utils.AnnotatorUtils
toEntity(String) - Method in class org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
toString() - Method in class org.molgenis.data.annotation.core.datastructures.Locus
TRANSCRIPT_BIOTYPE - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData

U

UiAnnotationException - Exception in org.molgenis.data.annotation.core.exception
UiAnnotationException(AnnotationException) - Constructor for exception org.molgenis.data.annotation.core.exception.UiAnnotationException
UnresolvedAnnotatorDependencyException - Exception in org.molgenis.data.annotation.core.exception
UnresolvedAnnotatorDependencyException() - Constructor for exception org.molgenis.data.annotation.core.exception.UnresolvedAnnotatorDependencyException
UnresolvedAnnotatorDependencyException(String) - Constructor for exception org.molgenis.data.annotation.core.exception.UnresolvedAnnotatorDependencyException
UnresolvedAnnotatorDependencyException(Throwable) - Constructor for exception org.molgenis.data.annotation.core.exception.UnresolvedAnnotatorDependencyException
UnresolvedAnnotatorDependencyException(String, Throwable) - Constructor for exception org.molgenis.data.annotation.core.exception.UnresolvedAnnotatorDependencyException

V

valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.AnnotatorInfo.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.AnnotatorInfo.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.GeneralizedInheritance: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Category: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Classification: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Method: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.data.annotation.core.entity.impl.snpeff.Impact: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.molgenis.data.annotation.core.entity.AnnotatorInfo.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.AnnotatorInfo.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.GeneralizedInheritance: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Category: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Classification: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Method: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.data.annotation.core.entity.impl.snpeff.Impact: Returns an array containing the constants of this enum type, in the order they are declared.
VARIANT - Static variable in class org.molgenis.data.annotation.core.effects.EffectsMetaData
VARIANT_FILE_LOCATION - Static variable in class org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings.Meta

W

withExtraSensitivity(int) - Method in class org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds

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