Hierarchy For All Packages

Package Hierarchies:

• org.molgenis.data.annotation.core,
• org.molgenis.data.annotation.core.datastructures,
• org.molgenis.data.annotation.core.effects,
• org.molgenis.data.annotation.core.entity,
• org.molgenis.data.annotation.core.entity.impl,
• org.molgenis.data.annotation.core.entity.impl.framework,
• org.molgenis.data.annotation.core.entity.impl.gavin,
• 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.exception,
• org.molgenis.data.annotation.core.filter,
• org.molgenis.data.annotation.core.query,
• org.molgenis.data.annotation.core.resources,
• org.molgenis.data.annotation.core.resources.impl,
• org.molgenis.data.annotation.core.resources.impl.emx,
• org.molgenis.data.annotation.core.resources.impl.tabix,
• org.molgenis.data.annotation.core.utils,
• org.molgenis.data.annotation.web,
• org.molgenis.data.annotation.web.bootstrap,
• org.molgenis.data.annotation.web.meta,
• org.molgenis.data.annotation.web.settings

Class Hierarchy

• java.lang.Object
  • org.molgenis.data.support.AbstractRepository (implements org.molgenis.data.Repository<E>)
    • org.molgenis.data.annotation.core.resources.impl.GeneCsvRepository
    • org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository
    • org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository
    • org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository
    • org.molgenis.data.vcf.VcfRepository
      • org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepository
  • org.molgenis.data.annotation.core.AbstractRepositoryAnnotator (implements org.molgenis.data.annotation.core.RepositoryAnnotator)
    • org.molgenis.data.annotation.core.AbstractRepositoryEntityAnnotator
      • org.molgenis.data.annotation.core.entity.impl.framework.RepositoryAnnotatorImpl
        • org.molgenis.data.annotation.core.EffectBasedAnnotator
    • org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator (implements org.molgenis.data.annotation.core.EffectCreatingAnnotator)
  • org.molgenis.data.AbstractSystemEntityFactory<E,M,P> (implements org.molgenis.data.EntityFactory<E,P>)
    • org.molgenis.data.annotation.web.meta.AnnotationJobExecutionFactory
  • org.molgenis.data.annotation.web.AnnotationServiceImpl (implements org.molgenis.data.annotation.web.AnnotationService)
  • org.molgenis.data.annotation.web.bootstrap.AnnotatorBootstrapper
  • org.molgenis.data.annotation.core.utils.AnnotatorDependencyOrderResolver
  • org.molgenis.data.annotation.core.entity.AnnotatorInfo
  • org.molgenis.data.annotation.core.utils.AnnotatorUtils
  • org.molgenis.data.annotation.core.query.AttributeEqualsQueryCreator (implements org.molgenis.data.annotation.core.entity.QueryCreator)
  • org.molgenis.data.annotation.core.entity.impl.CaddAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.CGDAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.filter.ClinvarMultiAllelicResultFilter (implements org.molgenis.data.annotation.core.entity.ResultFilter)
  • org.molgenis.data.annotation.core.utils.CmdLineAnnotatorUtils
  • org.molgenis.data.annotation.web.CrudRepositoryAnnotator
  • org.molgenis.data.annotation.core.entity.impl.DannAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.effects.EffectsMetaData (implements org.molgenis.data.annotation.web.meta.AnnotatorEntityType)
  • org.molgenis.data.annotation.core.utils.EffectStructureConverter
  • org.molgenis.data.annotation.core.entity.impl.ExacAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.filter.FirstResultFilter (implements org.molgenis.data.annotation.core.entity.ResultFilter)
  • org.molgenis.data.annotation.core.entity.impl.FitConAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm
  • org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds
  • org.molgenis.data.annotation.core.query.GeneNameQueryCreator (implements org.molgenis.data.annotation.core.entity.QueryCreator)
  • org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.hpo.HpoResultFilter (implements org.molgenis.data.annotation.core.entity.ResultFilter)
  • org.molgenis.data.annotation.core.resources.impl.emx.InMemoryRepositoryFactory (implements org.molgenis.data.annotation.core.resources.impl.RepositoryFactory)
  • org.molgenis.data.annotation.core.utils.JarRunnerImpl (implements org.molgenis.data.annotation.core.utils.JarRunner)
  • org.molgenis.data.annotation.core.utils.JsonReader
  • org.molgenis.data.annotation.core.entity.impl.gavin.Judgment
  • org.molgenis.data.annotation.core.datastructures.Location
  • org.molgenis.data.annotation.core.datastructures.Locus
  • org.molgenis.data.annotation.core.query.LocusQueryCreator (implements org.molgenis.data.annotation.core.entity.QueryCreator)
  • org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter (implements org.molgenis.data.annotation.core.entity.ResultFilter)
  • org.molgenis.data.annotation.core.resources.impl.MultiFileResource (implements org.molgenis.data.annotation.core.resources.Resource)
  • org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl (implements org.molgenis.data.annotation.core.resources.MultiResourceConfig)
  • org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.omim.OmimResultFilter (implements org.molgenis.data.annotation.core.entity.ResultFilter)
  • org.molgenis.data.annotation.core.entity.impl.framework.QueryAnnotatorImpl (implements org.molgenis.data.annotation.core.entity.EntityAnnotator)
    • org.molgenis.data.annotation.core.entity.impl.framework.AbstractAnnotator (implements org.molgenis.data.annotation.core.entity.EntityAnnotator)
  • org.molgenis.data.annotation.core.resources.impl.ResourceImpl (implements org.molgenis.data.annotation.core.resources.Resource)
    • org.molgenis.data.annotation.core.resources.impl.emx.EmxResourceImpl
  • org.molgenis.data.annotation.core.resources.impl.ResourcesImpl (implements org.molgenis.data.annotation.core.resources.Resources)
  • org.molgenis.data.annotation.web.settings.SingleFileLocationCmdLineAnnotatorSettingsConfigurer (implements org.molgenis.data.annotation.core.resources.CmdLineAnnotatorSettingsConfigurer)
  • org.molgenis.data.annotation.core.resources.impl.SingleResourceConfig (implements org.molgenis.data.annotation.core.resources.ResourceConfig)
  • org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner
  • org.molgenis.data.support.StaticEntity (implements org.molgenis.data.Entity)
    • org.molgenis.data.settings.DefaultSettingsEntity (implements org.molgenis.data.Entity)
      • org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.DannAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings
      • org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings
    • org.molgenis.data.meta.model.EntityType
      • org.molgenis.data.meta.SystemEntityType
        • org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData
        • org.molgenis.data.settings.DefaultSettingsEntityType
          • org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.DannAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings.Meta
          • org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta
    • org.molgenis.data.jobs.model.JobExecution
      • org.molgenis.data.annotation.web.meta.AnnotationJobExecution
  • org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader
  • org.molgenis.data.annotation.core.resources.impl.tabix.TabixReader.Iterator
  • org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepositoryFactory (implements org.molgenis.data.annotation.core.resources.impl.RepositoryFactory)
  • org.molgenis.data.annotation.core.resources.impl.tabix.TabixVcfRepositoryFactory (implements org.molgenis.data.annotation.core.resources.impl.RepositoryFactory)
  • org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator (implements org.molgenis.data.annotation.core.entity.AnnotatorConfig)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • org.molgenis.data.annotation.core.exception.AnnotationException
          • org.molgenis.data.annotation.core.exception.UiAnnotationException
        • org.molgenis.data.annotation.core.exception.UnresolvedAnnotatorDependencyException

Interface Hierarchy

• org.molgenis.data.annotation.web.AnnotationService
• org.molgenis.data.annotation.core.entity.Annotator
  • org.molgenis.data.annotation.core.entity.EntityAnnotator
• org.molgenis.data.annotation.core.entity.AnnotatorConfig
• org.molgenis.data.annotation.web.meta.AnnotatorEntityType
• org.molgenis.data.annotation.core.resources.CmdLineAnnotatorSettingsConfigurer
• org.molgenis.data.annotation.core.EffectCreatingAnnotator
• org.molgenis.data.annotation.core.entity.EntityProcessor
  • org.molgenis.data.annotation.core.entity.QueryCreator
  • org.molgenis.data.annotation.core.entity.ResultFilter
• org.molgenis.data.annotation.core.utils.JarRunner
• org.molgenis.data.annotation.core.resources.MultiResourceConfig
• org.molgenis.data.annotation.core.RepositoryAnnotator
• org.molgenis.data.annotation.core.resources.impl.RepositoryFactory
• org.molgenis.data.annotation.core.resources.Resource
• org.molgenis.data.annotation.core.resources.ResourceConfig
• org.molgenis.data.annotation.core.resources.Resources

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.molgenis.data.annotation.core.entity.AnnotatorInfo.Status
    • org.molgenis.data.annotation.core.entity.AnnotatorInfo.Type
    • org.molgenis.data.annotation.core.entity.impl.gavin.Category
    • org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Classification
    • org.molgenis.data.annotation.core.entity.impl.gavin.Judgment.Method
    • org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.GeneralizedInheritance
    • org.molgenis.data.annotation.core.entity.impl.CGDAnnotator.CGDAttributeName
    • org.molgenis.data.annotation.core.entity.impl.snpeff.Impact