Class Hierarchy (Gemma Core 2.0.0-alpha Test API)

Package Hierarchies:

Class Hierarchy

java.lang.Object
- org.springframework.security.acls.afterinvocation.AbstractAclProvider (implements org.springframework.security.access.AfterInvocationProvider)
  - org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
    - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationMapValueFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationOwnedCollectionFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationPrivateCollectionFilteringProvider
      - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectCollectionFilteringProvider
        
        ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapFilteringProvider
        
        ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectMapValueFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider
        
        ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectMapReadProvider
    - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCollectionFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
        
        ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceCollectionByArrayDesignFilteringProvider
        
        ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDataVectorCollectionByExpressionExperimentFilteringProvider
        
        ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationDifferentialExpressionAnalysisResultCollectionByResultSetFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationOwnedCollectionFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationPrivateCollectionFilteringProvider
  - org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationProvider (implements org.springframework.context.MessageSourceAware)
    - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider
    - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationByAssociationFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationCompositeSequenceByArrayDesignFilteringProvider
    - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationProvider
    - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider
    - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationValueObjectProvider
    - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectReadProvider
  - ubic.gemma.core.security.acl.afterinvocation.AclEntryAfterInvocationStreamFilteringProvider
  - ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationStreamFilteringProvider
- org.springframework.security.access.vote.AbstractAclVoter (implements org.springframework.security.access.AccessDecisionVoter<S>)
  - ubic.gemma.core.security.acl.voter.AclEntryCollectionVoter
    - ubic.gemma.core.security.acl.voter.AclEntryMapValueVoter
    - ubic.gemma.core.security.acl.voter.AclEntryMapVoter
  - org.springframework.security.acls.AclEntryVoter
    - ubic.gemma.core.security.acl.voter.AclEntryVoter
- ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
  - ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfigurer
- ubic.gemma.core.context.AbstractAsyncFactoryBean<T> (implements ubic.gemma.core.context.AsyncFactoryBean<T>, org.springframework.beans.factory.DisposableBean)
- org.springframework.security.web.authentication.AbstractAuthenticationTargetUrlRequestHandler
  - org.springframework.security.web.authentication.SimpleUrlAuthenticationSuccessHandler (implements org.springframework.security.web.authentication.AuthenticationSuccessHandler)
    - org.springframework.security.web.authentication.SavedRequestAwareAuthenticationSuccessHandler
      - ubic.gemma.core.security.authentication.AjaxAuthenticationSuccessHandler
- ubic.gemma.core.loader.util.mapper.AbstractBioAssayMapper (implements ubic.gemma.core.loader.util.mapper.BioAssayMapper)
  - ubic.gemma.core.loader.expression.geo.singleCell.GeoBioAssayMapper (implements ubic.gemma.core.loader.util.mapper.HintingEntityMapper<T>)
  - ubic.gemma.core.loader.util.mapper.SimpleBioAssayMapper (implements ubic.gemma.core.loader.util.mapper.HintingEntityMapper<T>)
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
  - java.util.AbstractList<E> (implements java.util.List<E>)
    - ubic.gemma.persistence.util.CursorPage<O> (implements java.util.List<E>)
    - ubic.gemma.persistence.util.Slice<O> (implements java.util.List<E>)
    - ubic.gemma.core.datastructure.sparse.SparseArrayList<T> (implements ubic.gemma.core.datastructure.sparse.SparseList<T>)
    - ubic.gemma.core.datastructure.sparse.SparseRangeArrayList<T> (implements ubic.gemma.core.datastructure.sparse.SparseList<T>)
  - java.util.AbstractSet<E> (implements java.util.Set<E>)
    - ubic.gemma.model.common.search.SearchResultSet<T>
- ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao.CriteriaContext<T,R>
- ubic.gemma.persistence.service.AbstractDao<T> (implements ubic.gemma.persistence.service.BaseDao<T>)
  - ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao<T> (implements ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao<T>)
    - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao)
    - ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDao)
    - ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao)
  - ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
    - ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>, org.springframework.beans.factory.InitializingBean)
      - ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao<O,VO>
        
        ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao)
        
        ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl (implements ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao)
      - ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
        
        ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<C,VO> (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
        
        ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl (implements ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao)
        
        ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao)
        
        ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl (implements ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao)
        
        ubic.gemma.persistence.service.genome.GeneDaoImpl (implements ubic.gemma.persistence.service.genome.GeneDao, org.springframework.beans.factory.InitializingBean)
        
        ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl (implements ubic.gemma.persistence.service.genome.taxon.TaxonDao)
    - ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao)
      - ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicDao)
      - ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl (implements ubic.gemma.persistence.service.common.description.DatabaseEntryDao)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueDao)
    - ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceDao)
    - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDao)
    - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl (implements ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao)
    - ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl (implements ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao)
    - ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl (implements ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao)
    - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao)
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao)
    - ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao)
    - ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.GeeqDao)
    - ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneProductDao)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao)
  - ubic.gemma.persistence.service.common.description.AnnotationRelationDaoImpl (implements ubic.gemma.persistence.service.common.description.AnnotationRelationDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao)
  - ubic.gemma.persistence.service.genome.ChromosomeDaoImpl (implements ubic.gemma.persistence.service.genome.ChromosomeDao)
  - ubic.gemma.persistence.service.expression.biomaterial.CompoundDaoImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.ContactDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDao)
  - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao)
  - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao)
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao)
  - ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseDao)
  - ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl (implements ubic.gemma.persistence.service.association.Gene2GOAssociationDao)
  - ubic.gemma.persistence.service.genome.gene.GeneAliasDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneAliasDao)
  - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao)
  - ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetDao)
  - ubic.gemma.persistence.service.genome.gene.GeneSetMemberDaoImpl (implements ubic.gemma.persistence.service.BaseDao<T>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao)
  - ubic.gemma.persistence.service.pipeline.PipelineJobBatchDaoImpl (implements ubic.gemma.persistence.service.pipeline.PipelineJobBatchDao)
  - ubic.gemma.persistence.service.pipeline.PipelineJobDaoImpl (implements ubic.gemma.persistence.service.pipeline.PipelineJobDao)
  - ubic.gemma.persistence.service.pipeline.PipelineJobEventDaoImpl (implements ubic.gemma.persistence.service.pipeline.PipelineJobEventDao)
  - ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao)
  - ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl (implements ubic.gemma.persistence.service.common.protocol.ProtocolDao)
  - ubic.gemma.persistence.service.common.description.PublicationAssociationDaoImpl (implements ubic.gemma.persistence.service.common.description.PublicationAssociationDao)
  - ubic.gemma.persistence.service.association.ReferenceAssociationDaoImpl (implements ubic.gemma.persistence.service.association.ReferenceAssociationDao)
  - ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao)
  - ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.StatementDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao)
  - ubic.gemma.persistence.service.common.measurement.UnitDaoImpl (implements ubic.gemma.persistence.service.common.measurement.UnitDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.UserDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao)
- ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader (implements ubic.gemma.core.loader.expression.DataLoader)
  - ubic.gemma.core.loader.expression.sequencing.AbstractDelegatingSequencingDataLoader (implements ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader)
    - ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader)
      - ubic.gemma.core.loader.expression.singleCell.metadata.GenericMetadataSingleCellDataLoader (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader)
      - ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoader
    - ubic.gemma.core.loader.expression.sequencing.SequencingMetadataFileDataLoader
- ubic.gemma.core.util.concurrent.AbstractDelegatingExecutor (implements ubic.gemma.core.util.concurrent.DelegatingExecutor)
  - ubic.gemma.core.util.concurrent.AbstractDelegatingExecutorService (implements ubic.gemma.core.util.concurrent.DelegatingExecutorService)
    - ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutorService
    - ubic.gemma.core.logging.log4j.DelegatingThreadContextScheduledExecutorService (implements ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService)
- ubic.gemma.core.ontology.providers.AbstractDelegatingOntologyService (implements ubic.gemma.core.ontology.providers.OntologyService)
  - ubic.gemma.core.ontology.providers.AbstractBaseCodeOntologyService
    - ubic.gemma.core.ontology.providers.CellLineOntologyService
    - ubic.gemma.core.ontology.providers.CellTypeOntologyService
    - ubic.gemma.core.ontology.providers.ExperimentalFactorOntologyService
    - ubic.gemma.core.ontology.providers.GenotypeOntologyService
    - ubic.gemma.core.ontology.providers.HumanDevelopmentOntologyService
    - ubic.gemma.core.ontology.providers.HumanPhenotypeOntologyService
    - ubic.gemma.core.ontology.providers.MammalianPhenotypeOntologyService
    - ubic.gemma.core.ontology.providers.MouseDevelopmentOntologyService
    - ubic.gemma.core.ontology.providers.NeuroBehaviorOntologyService
    - ubic.gemma.core.ontology.providers.ObiService
    - ubic.gemma.core.ontology.providers.SequenceOntologyService
    - ubic.gemma.core.ontology.providers.UberonOntologyService
    - ubic.gemma.core.ontology.providers.UnitsOntologyService
  - ubic.gemma.core.ontology.providers.GemmaOntologyService
  - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl (implements ubic.gemma.core.ontology.providers.GeneOntologyService, org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.core.ontology.providers.GenericOntologyService
  - ubic.gemma.core.ontology.providers.MedicOntologyService
  - ubic.gemma.core.ontology.providers.PatoOntologyService
- ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>)
  - ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix<T>)
    - ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix (implements ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix)
    - ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix (implements ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveIntMatrix)
    - ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix
  - ubic.gemma.core.datastructure.matrix.AbstractMultiAssayExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>, ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix<T>)
    - ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
    - ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
    - ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix (implements ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix, ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix<T>)
    - ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
    - ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
  - ubic.gemma.core.datastructure.matrix.AbstractSingleCellExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix<T>)
    - ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataDoubleMatrix (implements ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix)
    - ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix (implements ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix)
  - ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>)
- org.springframework.beans.factory.config.AbstractFactoryBean<T> (implements org.springframework.beans.factory.BeanClassLoaderAware, org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.core.security.authentication.ManualAuthenticationServiceBasedSecurityContextFactory
  - ubic.gemma.core.ontology.providers.OntologyServiceFactory<T>
  - ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
- ubic.gemma.core.loader.util.fetcher.AbstractFetcher (implements ubic.gemma.core.loader.util.fetcher.Fetcher)
  - ubic.gemma.core.loader.util.fetcher.FtpFetcher
    - ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher (implements ubic.gemma.core.loader.util.fetcher.ArchiveFetcher)
      - ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
      - ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
      - ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
      - ubic.gemma.core.loader.genome.taxon.TaxonFetcher
    - ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
      - ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
        
        ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
      - ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
      - ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
        
        ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
    - ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
    - ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
  - ubic.gemma.core.loader.util.fetcher.HttpFetcher
- ubic.gemma.core.loader.util.fetcher2.AbstractFetcher
  - ubic.gemma.core.loader.expression.cellxgene.CellXGeneFetcher
  - ubic.gemma.core.loader.expression.geo.fetcher2.GeoFetcher
- ubic.gemma.core.util.matrix.datafilter.AbstractFilter<M,R,C,V> (implements ubic.gemma.core.util.matrix.datafilter.Filter<M,R,C,V>)
  - ubic.gemma.core.util.matrix.datafilter.RowMissingFilter<M,R,C,V>
- org.apache.logging.log4j.core.filter.AbstractFilterable.Builder<B>
  - org.apache.logging.log4j.core.appender.AbstractAppender.Builder<B>
    - ubic.gemma.core.logging.log4j.ProgressUpdateAppender.Builder (implements org.apache.logging.log4j.core.util.Builder<T>)
    - ubic.gemma.core.logging.log4j.SlackAppender.Builder (implements org.apache.logging.log4j.core.util.Builder<T>)
- ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
- ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
- ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder
- ubic.gemma.core.loader.util.ftp.AbstractFTPClientAuthenticator (implements ubic.gemma.core.loader.util.ftp.FTPClientAuthenticator)
  - ubic.gemma.core.loader.util.ftp.AnonymousFTPCLientAuthenticator
  - ubic.gemma.core.loader.util.ftp.UsernamePasswordFTPClientAuthenticator
- ubic.gemma.core.loader.util.mapper.AbstractGeneIdentifierBasedDesignElementMapper<K> (implements ubic.gemma.core.loader.util.mapper.DesignElementMapper)
  - ubic.gemma.core.loader.util.mapper.EnsemblIdDesignElementMapper
  - ubic.gemma.core.loader.util.mapper.GeneNameDesignElementMapper
  - ubic.gemma.core.loader.util.mapper.NcbiIdDesignElementMapper
  - ubic.gemma.core.loader.util.mapper.OfficialSymbolDesignElementMapper
- ubic.gemma.model.common.AbstractIdentifiable (implements ubic.gemma.model.common.Identifiable)
  - ubic.gemma.model.common.AbstractDescribable (implements ubic.gemma.model.common.Describable)
    - ubic.gemma.model.common.auditAndSecurity.AbstractAuditable (implements ubic.gemma.model.common.auditAndSecurity.Auditable)
      - ubic.gemma.model.expression.arrayDesign.ArrayDesign (implements ubic.gemma.model.common.auditAndSecurity.curation.Curatable, ubic.gemma.model.common.auditAndSecurity.SecuredNotChild)
      - ubic.gemma.model.analysis.expression.ExpressionExperimentSet (implements ubic.gemma.model.common.auditAndSecurity.Securable)
      - ubic.gemma.model.genome.gene.GeneSet (implements ubic.gemma.model.common.auditAndSecurity.SecuredNotChild)
      - ubic.gemma.model.analysis.Investigation (implements ubic.gemma.model.common.auditAndSecurity.Securable)
        
        ubic.gemma.model.expression.experiment.BioAssaySet
        
        ubic.gemma.model.expression.experiment.ExpressionExperiment (implements ubic.gemma.model.common.auditAndSecurity.curation.Curatable, ubic.gemma.model.common.auditAndSecurity.SecuredNotChild)
        
        ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
        
        ubic.gemma.model.expression.experiment.PreboardedExperiment
      - ubic.gemma.model.pipeline.PipelineJobBatch
      - ubic.gemma.model.common.auditAndSecurity.curation.Ticket
      - ubic.gemma.model.common.auditAndSecurity.UserGroup (implements ubic.gemma.core.security.model.UserGroup)
    - ubic.gemma.model.analysis.Analysis
      - ubic.gemma.model.expression.bioAssayData.CellTypeAssignment (implements ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics)
      - ubic.gemma.model.analysis.expression.ExpressionAnalysis
        
        ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis (implements ubic.gemma.model.common.auditAndSecurity.Securable)
        
        ubic.gemma.model.analysis.SingleExperimentAnalysis<T> (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
        
        ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis
        
        ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis
        
        ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
    - ubic.gemma.model.common.description.BibliographicReference
    - ubic.gemma.model.expression.bioAssay.BioAssay (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
    - ubic.gemma.model.expression.biomaterial.BioMaterial (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
    - ubic.gemma.model.genome.biosequence.BioSequence
    - ubic.gemma.model.blacklist.BlacklistedEntity
      - ubic.gemma.model.blacklist.BlacklistedExperiment
      - ubic.gemma.model.blacklist.BlacklistedPlatform
    - ubic.gemma.model.common.description.Characteristic (implements java.lang.Comparable<T>)
      - ubic.gemma.model.expression.experiment.Statement
    - ubic.gemma.model.genome.ChromosomeFeature
      - ubic.gemma.model.genome.Gene
      - ubic.gemma.model.genome.gene.GeneProduct
    - ubic.gemma.model.expression.designElement.CompositeSequence
    - ubic.gemma.model.expression.biomaterial.Compound
    - ubic.gemma.model.common.auditAndSecurity.Contact
      - ubic.gemma.model.common.auditAndSecurity.Person
        
        ubic.gemma.model.common.auditAndSecurity.User (implements ubic.gemma.core.security.model.User)
    - ubic.gemma.model.expression.experiment.ExperimentalDesign (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
    - ubic.gemma.model.expression.experiment.ExperimentalFactor (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
    - ubic.gemma.model.common.description.ExternalDatabase (implements ubic.gemma.model.common.auditAndSecurity.Auditable, ubic.gemma.model.common.description.Versioned)
    - ubic.gemma.model.expression.bioAssayData.GenericCellLevelCharacteristics (implements ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics)
    - ubic.gemma.model.common.protocol.Protocol (implements ubic.gemma.model.common.auditAndSecurity.Securable)
    - ubic.gemma.model.common.quantitationtype.QuantitationType
    - ubic.gemma.core.loader.expression.arrayDesign.Reporter (implements java.io.Serializable)
    - ubic.gemma.model.expression.biomaterial.Treatment
  - ubic.gemma.model.expression.arrayDesign.AlternateName
  - ubic.gemma.model.common.description.AnnotationRelation
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetDisposition
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetTriage
  - ubic.gemma.model.common.auditAndSecurity.AuditEvent
  - ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
    - ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.TagAddedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.TagRemovedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationSetEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionAlteringEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagAlteringEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.DatasetPublishedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DesignChangeEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
      - ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsAddedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.CellLevelCharacteristicsRemovedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentAddedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.CellTypeAssignmentRemovedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.PreferredCellTypeAssignmentChangedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.AggregatedSingleDataAddedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.RawDataAddedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataAddedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.RawDataRemovedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataRemovedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.RawDataReplacedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellDataReplacedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DatasetShortNameChangedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.FailedPipelineRunEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PipelineRunEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PreferredDataChangedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.PreferredRawDataChangedEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.PreferredSingleCellDataChangedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent
        
        ubic.gemma.model.common.auditAndSecurity.eventType.VectorsReorderedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.SingleCellSubSetsCreatedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchCancelledEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchClosedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.PipelineBatchSubmittedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.PreboardedCreatedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.PreboardedPromotedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TicketAssignedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TicketMetadataChangedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TicketOpenedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TicketStateChangedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TicketTargetStatusChangedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.WorkflowStateChangedEvent
  - ubic.gemma.model.common.auditAndSecurity.AuditTrail
  - ubic.gemma.model.common.description.BibRefAnnotation
    - ubic.gemma.model.common.description.Keyword
    - ubic.gemma.model.common.description.MedicalSubjectHeading
  - ubic.gemma.model.expression.bioAssayData.BioAssayDimension
  - ubic.gemma.model.association.BioSequence2GeneProduct
    - ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
    - ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
    - ubic.gemma.model.association.ReferenceAssociation
  - ubic.gemma.model.genome.Chromosome
  - ubic.gemma.model.genome.ChromosomeLocation
    - ubic.gemma.model.genome.PhysicalLocation
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDecision
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails
  - ubic.gemma.model.common.description.DatabaseEntry
  - ubic.gemma.model.expression.bioAssayData.DataVector
    - ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
      - ubic.gemma.model.expression.bioAssayData.BulkExpressionDataVector
        
        ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
        
        ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
      - ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVector
  - ubic.gemma.model.analysis.expression.pca.Eigenvalue
  - ubic.gemma.model.analysis.expression.pca.Eigenvector
  - ubic.gemma.model.expression.experiment.FactorValue (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
  - ubic.gemma.model.expression.experiment.Geeq
  - ubic.gemma.model.association.Gene2GOAssociation
  - ubic.gemma.model.genome.gene.GeneAlias
  - ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult
  - ubic.gemma.model.genome.gene.GeneSetMember
  - ubic.gemma.model.common.auditAndSecurity.GroupAuthority (implements ubic.gemma.core.security.model.GroupAuthority)
  - ubic.gemma.model.analysis.expression.diff.HitListSize
  - ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
  - ubic.gemma.model.common.measurement.Measurement
  - ubic.gemma.model.genome.gene.Multifunctionality
  - ubic.gemma.model.pipeline.PipelineJob
  - ubic.gemma.model.pipeline.PipelineJobEvent
  - ubic.gemma.model.analysis.expression.pca.ProbeLoading
  - ubic.gemma.model.common.description.PublicationAssociation
  - ubic.gemma.model.analysis.expression.diff.PvalueDistribution
  - ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix
  - ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult
    - ubic.gemma.model.genome.sequenceAnalysis.BlatResult
  - ubic.gemma.model.expression.bioAssayData.SingleCellDimension (implements ubic.gemma.model.common.Identifiable)
  - ubic.gemma.model.expression.bioAssayData.SingleCellDimensionExperiment
  - ubic.gemma.model.genome.Taxon
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget
  - ubic.gemma.model.common.measurement.Unit
- ubic.gemma.core.ontology.lexical.AbstractLexicalOntologyService (implements ubic.gemma.core.ontology.providers.OntologyService)
  - ubic.gemma.core.ontology.providers.CellosaurusOntologyService
  - ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService
  - ubic.gemma.core.ontology.providers.MgiStrainOntologyService
- org.apache.logging.log4j.core.AbstractLifeCycle (implements org.apache.logging.log4j.core.LifeCycle2)
  - org.apache.logging.log4j.core.filter.AbstractFilterable (implements org.apache.logging.log4j.core.filter.Filterable)
    - org.apache.logging.log4j.core.appender.AbstractAppender (implements org.apache.logging.log4j.core.Appender, org.apache.logging.log4j.core.impl.LocationAware)
      - ubic.gemma.core.logging.log4j.ProgressUpdateAppender
      - ubic.gemma.core.logging.log4j.SlackAppender
- ubic.gemma.core.util.matrix.AbstractMatrix<R,C,V> (implements ubic.gemma.core.util.matrix.Matrix2D<R,C,V>, java.io.Serializable)
  - ubic.gemma.core.util.matrix.DoubleMatrix<R,C> (implements ubic.gemma.core.util.matrix.PrimitiveMatrix<R,C,V>)
    - ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix<R,C>
    - ubic.gemma.core.util.matrix.DenseDoubleMatrix<R,C>
    - ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix<R,C>
    - ubic.gemma.core.util.matrix.SparseDoubleMatrix<R,C>
  - ubic.gemma.core.util.matrix.IntegerMatrix<R,C> (implements ubic.gemma.core.util.matrix.PrimitiveMatrix<R,C,V>)
  - ubic.gemma.core.util.matrix.ObjectMatrixImpl<R,C,V> (implements ubic.gemma.core.util.matrix.ObjectMatrix<R,C,V>)
  - ubic.gemma.core.util.matrix.StringMatrix<R,C> (implements ubic.gemma.core.util.matrix.ObjectMatrix<R,C,V>)
- ubic.gemma.core.util.matrix.AbstractMatrixReader<M,V>
  - ubic.gemma.core.util.matrix.DoubleMatrixReader
  - ubic.gemma.core.util.matrix.StringMatrixReader
- ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
  - ubic.gemma.core.metrics.MeterRegistryJCacheConfigurer
- ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
  - ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer
  - ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer
- ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple (implements ubic.gemma.core.ontology.model.OntologyResource, java.io.Serializable)
  - ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty (implements ubic.gemma.core.ontology.model.AnnotationProperty)
  - ubic.gemma.core.ontology.simple.OntologyIndividualSimple (implements ubic.gemma.core.ontology.model.OntologyIndividual)
  - ubic.gemma.core.ontology.simple.OntologyPropertySimple (implements ubic.gemma.core.ontology.model.OntologyProperty)
  - ubic.gemma.core.ontology.simple.OntologyTermSimple (implements ubic.gemma.core.ontology.model.OntologyTerm)
    - ubic.gemma.core.ontology.lexical.LexicalOntologyTerm
- ubic.gemma.core.ontology.jena.AbstractOntologyService (implements ubic.gemma.core.ontology.providers.OntologyService)
  - ubic.gemma.core.ontology.jena.ClasspathOntologyService
  - ubic.gemma.core.ontology.jena.TdbOntologyService
  - ubic.gemma.core.ontology.jena.UrlOntologyService
    - ubic.gemma.core.ontology.providers.ChebiOntologyService (implements ubic.gemma.core.ontology.providers.SlimmableOntologyService)
    - ubic.gemma.core.ontology.providers.MondoOntologyService (implements ubic.gemma.core.ontology.providers.SlimmableOntologyService)
- ubic.gemma.core.util.AbstractProgressReporter (implements ubic.gemma.core.util.ProgressReporter)
  - ubic.gemma.core.util.LoggingProgressReporter (implements ubic.gemma.core.util.ProgressReporter)
- ubic.gemma.core.loader.expression.singleCell.transform.AbstractScriptBasedTransformation (implements ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformation)
  - ubic.gemma.core.loader.expression.singleCell.transform.AbstractCellRangerBasedTransformation (implements ubic.gemma.core.loader.expression.singleCell.transform.CellRangerBasedTransformation)
    - ubic.gemma.core.loader.expression.singleCell.transform.SingleCell10xMexFilter (implements ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation)
  - ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedTransformation (implements ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation)
    - ubic.gemma.core.loader.expression.singleCell.transform.AbstractPythonScriptBasedAnnDataTransformation (implements ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation)
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataPack
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataRewrite
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSample
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSortBySample
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataSparsify
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTranspose
      - ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataUnraw
- ubic.gemma.persistence.service.AbstractService<O> (implements ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.bioAssayData.AbstractBulkExpressionDataVectorService<T> (implements ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService<T>)
    - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService)
    - ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService)
    - ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService)
  - ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<O,VO> (implements ubic.gemma.persistence.service.BaseService<O>, ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl (implements ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService)
    - ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayService)
    - ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicService)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl (implements ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService)
    - ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl (implements ubic.gemma.persistence.service.common.description.DatabaseEntryService)
    - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService)
    - ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueService)
    - ubic.gemma.persistence.service.genome.gene.GeneServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneService)
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl (implements ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService)
    - ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl (implements ubic.gemma.persistence.service.genome.taxon.TaxonService)
  - ubic.gemma.persistence.service.AbstractVoEnabledService<O,VO> (implements ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceService, org.springframework.beans.factory.InitializingBean)
    - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService)
    - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService)
    - ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl (implements ubic.gemma.persistence.service.genome.biosequence.BioSequenceService)
    - ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl (implements ubic.gemma.persistence.service.blacklist.BlacklistedEntityService)
    - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService)
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService)
    - ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.GeeqService)
    - ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneProductService)
    - ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetService)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService)
  - ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService)
  - ubic.gemma.persistence.service.genome.ChromosomeServiceImpl (implements ubic.gemma.persistence.service.genome.ChromosomeService)
  - ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundService)
  - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService)
  - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService)
  - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService)
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService)
  - ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseService)
  - ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl (implements ubic.gemma.persistence.service.association.Gene2GOAssociationService)
  - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService)
  - ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService)
  - ubic.gemma.persistence.service.common.protocol.ProtocolServiceImpl (implements ubic.gemma.persistence.service.common.protocol.ProtocolService)
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService)
- ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleCellDetector (implements ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector)
  - ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleFileInSeriesSingleCellDetector
    - ubic.gemma.core.loader.expression.geo.singleCell.AbstractSingleH5FileInSeriesSingleCellDetector
      - ubic.gemma.core.loader.expression.geo.singleCell.AnnDataDetector (implements ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector)
      - ubic.gemma.core.loader.expression.geo.singleCell.SeuratDiskDetector
    - ubic.gemma.core.loader.expression.geo.singleCell.LoomSingleCellDetector
  - ubic.gemma.core.loader.expression.geo.singleCell.MexDetector (implements ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector, ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector)
- ubic.gemma.core.job.AbstractTask<C> (implements ubic.gemma.core.job.Task<C>)
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl (implements ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTask)
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl (implements ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTask)
  - ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskImpl (implements ubic.gemma.core.tasks.maintenance.ArrayDesignReportTask)
  - ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTask)
  - ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTask)
  - ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl (implements ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTask)
  - ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImpl (implements ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTask)
  - ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl (implements ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTask)
  - ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskImpl (implements ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTask)
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTask)
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTask)
  - ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskImpl (implements ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTask)
  - ubic.gemma.core.tasks.analysis.expression.GeeqTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.GeeqTask)
  - ubic.gemma.core.tasks.maintenance.GeoScrapeTaskImpl (implements ubic.gemma.core.tasks.maintenance.GeoScrapeTask)
  - ubic.gemma.core.tasks.maintenance.IndexerTaskImpl (implements ubic.gemma.core.tasks.maintenance.IndexerTask)
  - ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskImpl (implements ubic.gemma.core.tasks.maintenance.MultifunctionalityTask)
  - ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskImpl (implements ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTask)
  - ubic.gemma.core.tasks.analysis.expression.PreprocessTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.PreprocessExperimentTask)
  - ubic.gemma.core.tasks.analysis.expression.SvdTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.SvdTask)
  - ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
- org.springframework.security.authentication.dao.AbstractUserDetailsAuthenticationProvider (implements org.springframework.security.authentication.AuthenticationProvider, org.springframework.beans.factory.InitializingBean, org.springframework.context.MessageSourceAware)
  - org.springframework.security.authentication.dao.DaoAuthenticationProvider
    - ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider
- ubic.gemma.core.security.acl.AclAuthorizationStrategyImpl (implements org.springframework.security.acls.domain.AclAuthorizationStrategy)
- ubic.gemma.persistence.util.AclClassIdInitializer (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.security.authorization.acl.AclClassMetadata
- ubic.gemma.core.security.acl.domain.AclDaoImpl (implements ubic.gemma.core.security.acl.domain.AclDao)
- ubic.gemma.core.security.acl.domain.AclEntry (implements org.springframework.security.acls.model.AccessControlEntry, java.lang.Comparable<T>)
- ubic.gemma.core.security.acl.AclEventListener (implements org.hibernate.event.spi.PostDeleteEventListener, org.hibernate.event.spi.PostInsertEventListener)
- ubic.gemma.core.security.acl.AclEventListenerConfig (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.security.acl.domain.AclImpl (implements org.springframework.security.acls.model.OwnershipAcl)
- ubic.gemma.core.security.authorization.acl.AclLinterConfig
- ubic.gemma.core.security.authorization.acl.AclLinterConfig.AclLinterConfigBuilder
- ubic.gemma.core.security.authorization.acl.AclLinterHelperServiceImpl (implements ubic.gemma.core.security.authorization.acl.AclLinterHelperService)
- ubic.gemma.core.security.authorization.acl.AclLinterService.LintResult
- ubic.gemma.core.security.authorization.acl.AclLinterServiceImpl (implements ubic.gemma.core.security.authorization.acl.AclLinterService)
- ubic.gemma.core.security.acl.domain.AclObjectIdentity (implements org.springframework.security.acls.model.ObjectIdentity)
- ubic.gemma.persistence.util.AclQueryUtils
- ubic.gemma.core.security.acl.domain.AclServiceImpl (implements ubic.gemma.core.security.acl.domain.AclService)
- ubic.gemma.core.security.acl.domain.AclSid (implements java.io.Serializable)
  - ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid
  - ubic.gemma.core.security.acl.domain.AclPrincipalSid
- ubic.gemma.core.security.acl.AclSidRetrievalStrategyImpl (implements org.springframework.security.acls.model.SidRetrievalStrategy)
- ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManager (implements org.springframework.security.authorization.AuthorizationManager<T>)
- ubic.gemma.core.security.authorization.acl.AclVoterAuthorizationManagerConfig
- ubic.gemma.core.security.util.ActingIdentity
- ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
- ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
- ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.model.expression.arrayDesign.AlternateName.Factory
- ubic.gemma.model.analysis.AnalysisResult (implements ubic.gemma.model.common.Identifiable)
  - ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult
- ubic.gemma.model.analysis.AnalysisResultSet<R> (implements ubic.gemma.model.common.Identifiable)
  - ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet<R>
    - ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT>)
- ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl (implements ubic.gemma.core.analysis.expression.AnalysisUtilService)
- ubic.gemma.core.loader.util.anndata.AnnData (implements java.io.Closeable)
- ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader)
  - ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader
- ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
- ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadService)
- ubic.gemma.core.config.AnnotationDrivenSchedulingConfig
- ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationQuery
- ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary
- ubic.gemma.persistence.service.common.description.AnnotationRelationDao.RelationSummary.RelationSummaryBuilder
- ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl (implements ubic.gemma.persistence.service.common.description.AnnotationRelationService)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService)
- ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetPayloadCounts
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.AttachedAnnotationSet
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService.RunProvenance
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService)
- ubic.gemma.core.util.math.linearmodels.AnovaEffect (implements java.io.Serializable)
- ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
- ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl (implements ubic.gemma.core.analysis.service.ArrayDesignAnnotationService)
- ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl (implements ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService)
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditService)
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService)
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService)
- ubic.gemma.persistence.persister.ArrayDesignPersister
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService)
- ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl (implements ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService)
- ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl (implements ubic.gemma.core.analysis.report.ArrayDesignReportService)
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService)
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService)
- ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
- ubic.gemma.core.loader.expression.arrayExpress.ArrayExpressUtils
- ubic.gemma.core.util.ArrayUtils
- ubic.gemma.core.security.audit.AuditedAspect
- ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory
- ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService)
- ubic.gemma.core.security.audit.AuditLogger
- ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
- ubic.gemma.persistence.audit.AuditTrailEventListener (implements org.hibernate.event.spi.PersistEventListener, org.hibernate.event.spi.PostInsertEventListener, org.hibernate.event.spi.PreDeleteEventListener)
- ubic.gemma.persistence.audit.AuditTrailEventListenerConfig (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.security.AuthorityConstants
- ubic.gemma.core.security.acl.BaseAclAdvice
  - ubic.gemma.core.security.authorization.acl.AclAdvice
- ubic.gemma.core.config.BaseCodeConfigurer (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
- org.apache.commons.configuration2.event.BaseEventSource (implements org.apache.commons.configuration2.event.EventSource)
  - org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
    - ubic.gemma.core.config.PropertySourcesConfiguration (implements org.apache.commons.configuration2.Configuration)
- ubic.gemma.model.analysis.expression.diff.Baseline
- ubic.gemma.core.analysis.expression.diff.BaselineSelection
- ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor (implements ubic.gemma.core.analysis.preprocess.batcheffects.ScanDateExtractor)
  - ubic.gemma.core.analysis.preprocess.batcheffects.AffyScanDateExtractor
  - ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor
  - ubic.gemma.core.analysis.preprocess.batcheffects.GenericScanFileDateExtractor
- ubic.gemma.model.common.BaseValueObject (implements java.io.Serializable)
- ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
  - ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
  - ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
  - ubic.gemma.core.loader.util.parser.LineMapParser<K,T>
    - ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
  - ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
  - ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
  - ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
  - ubic.gemma.core.loader.genome.ProbeSequenceParser
  - ubic.gemma.core.loader.genome.taxon.TaxonParser
- ubic.gemma.core.loader.util.parser.BasicLineParser<T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
  - ubic.gemma.core.loader.genome.BlatResultParser
  - ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
  - ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
  - ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService)
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService)
- ubic.gemma.core.context.BeanFactoryUtils
- ubic.gemma.core.profiling.BeanInitializationTimeMonitor (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
- ubic.gemma.core.context.BeanNameGenerator (implements org.springframework.beans.factory.support.BeanNameGenerator)
- ubic.gemma.model.common.description.BibliographicReference.Factory
- ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService)
- ubic.gemma.persistence.hibernate.BinaryFunctionContributor (implements org.hibernate.boot.model.FunctionContributor)
- ubic.gemma.model.expression.bioAssay.BioAssay.Factory
- ubic.gemma.model.expression.bioAssay.BioAssayCategories
- ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
- ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService)
- ubic.gemma.model.expression.bioAssay.BioAssayUtils
- ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
- ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
- ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
- ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService)
- ubic.gemma.persistence.service.expression.biomaterial.BioMaterialUtils
- ubic.gemma.model.genome.biosequence.BioSequence.Factory
- ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadServiceImpl (implements ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService)
- ubic.gemma.persistence.util.BitwiseUtils
- ubic.gemma.core.util.math.linalg.Blas
- ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation.Factory
- ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadService)
- ubic.gemma.core.analysis.sequence.BlatAssociationScorer
- ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Factory
- ubic.gemma.core.analysis.sequence.BlatResult2Psl
- ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadService)
- ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>)
- ubic.gemma.core.geoscrape.BrainKeywordMatcher (implements ubic.gemma.core.geoscrape.GeoRecordMatcher)
- ubic.gemma.core.util.BuildInfo (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.logging.log4j.BuildInfoThreadContextPopulator (implements ubic.gemma.core.logging.log4j.ThreadContextPopulator)
- ubic.gemma.core.analysis.preprocess.slice.BulkDataSlicerUtils
- ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrixUtils
- ubic.gemma.persistence.util.BusinessKey
- ubic.gemma.persistence.util.ByteArrayConverter
- ubic.gemma.persistence.hibernate.ByteArrayType (implements org.hibernate.usertype.ParameterizedType, org.hibernate.usertype.UserType<J>)
- ubic.gemma.persistence.util.ByteArrayUtils
- ubic.gemma.persistence.cache.CacheUtils
- ubic.gemma.core.loader.util.anndata.CategoricalArray<T> (implements ubic.gemma.core.loader.util.anndata.Array<T>)
- ubic.gemma.model.common.description.Categories
- ubic.gemma.model.common.description.Category
- ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
- ubic.gemma.core.visualization.cellbrowser.CellBrowserServiceImpl (implements ubic.gemma.core.visualization.cellbrowser.CellBrowserService)
- ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixReader
- ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter (implements ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter)
- ubic.gemma.core.datastructure.matrix.CellBrowserTabularMetadataReader
- ubic.gemma.core.visualization.cellbrowser.CellBrowserUtils
- ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics.Factory
- ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils
- ubic.gemma.core.loader.expression.singleCell.metadata.CellLevelCharacteristicsWriter
- ubic.gemma.core.ontology.relation.CellosaurusRelationProducer
- ubic.gemma.model.expression.bioAssayData.CellTypeAssignment.Factory
- ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
- ubic.gemma.core.loader.expression.cellxgene.CellXGeneConverter
- ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderServiceImpl (implements ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderService)
- ubic.gemma.core.loader.expression.cellxgene.CellXGeneUtils
- ubic.gemma.core.loader.util.mapper.ChainedEntityMapper<T> (implements ubic.gemma.core.loader.util.mapper.EntityMapper<T>)
- ubic.gemma.persistence.util.ChannelUtils
- ubic.gemma.model.common.description.Characteristic.Factory
- ubic.gemma.persistence.service.common.description.CharacteristicDao.PriorCurationUsage
- ubic.gemma.persistence.service.common.description.CharacteristicDao.UsageExample
- ubic.gemma.persistence.service.common.description.CharacteristicReadServiceImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicReadService)
- ubic.gemma.model.common.description.CharacteristicUtils
- ubic.gemma.core.visualization.ChartThemeUtils
- ubic.gemma.core.visualization.ChartUtils
- ubic.gemma.core.ontology.providers.chebi.ChebiSeedResolver
- ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl (implements ubic.gemma.core.ontology.chembl.ChemblCodeResolver)
- ubic.gemma.core.ontology.chembl.ChemblCompound (implements java.io.Serializable)
- ubic.gemma.model.genome.Chromosome.Factory
- ubic.gemma.persistence.service.genome.ChromosomeUtils
- ubic.gemma.model.common.description.CitationValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.core.ontology.relation.ClInferredLocationProducer
- ubic.gemma.core.loader.expression.cellxgene.model.CollectionMetadata
- ubic.gemma.core.util.graphics.ColorMap
- ubic.gemma.core.util.graphics.ColorMatrix<A,B> (implements java.lang.Cloneable)
- ubic.gemma.persistence.persister.CommonPersister
- ubic.gemma.persistence.util.CommonQueries
- java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
  - java.awt.Container
    - javax.swing.JComponent (implements java.io.Serializable)
      - javax.swing.JPanel (implements javax.accessibility.Accessible)
        
        ubic.gemma.core.util.graphics.MatrixDisplay<R,C>
- ubic.gemma.core.config.ComponentScanConfig
- org.springframework.jdbc.datasource.init.CompositeDatabasePopulator (implements org.springframework.jdbc.datasource.init.DatabasePopulator)
  - ubic.gemma.persistence.initialization.DatabaseSchemaPopulator
  - ubic.gemma.persistence.initialization.InitialDataPopulator
- ubic.gemma.core.metrics.CompositeMeterRegistryFactory
- ubic.gemma.core.search.source.CompositeSearchSource (implements ubic.gemma.core.search.SearchSource)
- ubic.gemma.model.expression.designElement.CompositeSequence.Factory
- ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
- ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
- ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl (implements ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService)
- ubic.gemma.model.expression.biomaterial.Compound.Factory
- ubic.gemma.persistence.hibernate.CompressedStringListType (implements org.hibernate.usertype.ParameterizedType, org.hibernate.usertype.UserType<J>)
- ubic.gemma.core.datastructure.sparse.CompRowMatrixUtils
- ubic.gemma.core.config.Configuration
- ubic.gemma.core.config.ConfigUtils
- ubic.gemma.core.util.ConfigUtils
- ubic.gemma.core.util.Constants
- ubic.gemma.core.util.math.Constants
- ubic.gemma.model.common.auditAndSecurity.Contact.Factory
- ubic.gemma.model.common.auditAndSecurity.ContactUtils
- ubic.gemma.model.analysis.expression.diff.Contrast
- ubic.gemma.model.analysis.expression.diff.ContrastResult (implements ubic.gemma.model.common.Identifiable)
- ubic.gemma.model.analysis.expression.diff.ContrastResult.Factory
- ubic.gemma.model.analysis.expression.diff.ContrastsValueObject (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.ContrastVO (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Coordinate
- ubic.gemma.core.util.math.CorrelationStats
- ubic.gemma.persistence.initialization.CreateDatabasePopulator (implements org.springframework.jdbc.datasource.init.DatabasePopulator)
- ubic.gemma.core.loader.crossref.CrossRefFetcher
- ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest
- ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.SampleCharacteristicAdd
- ubic.gemma.persistence.service.expression.experiment.CurationCommitRequest.TagAdd
- ubic.gemma.persistence.service.expression.experiment.CurationCommitResult
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService)
- ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions
- ubic.gemma.model.common.auditAndSecurity.curation.CurationLock (implements java.io.Serializable)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService)
- ubic.gemma.persistence.util.Cursor
- ubic.gemma.model.common.description.DatabaseEntry.Factory
- ubic.gemma.persistence.service.common.description.DatabaseEntryReadServiceImpl (implements ubic.gemma.persistence.service.common.description.DatabaseEntryReadService)
- ubic.gemma.persistence.initialization.DatabaseSchemaUpdatePopulator (implements org.springframework.jdbc.datasource.init.DatabasePopulator)
- ubic.gemma.core.search.source.DatabaseSearchSource (implements org.springframework.core.Ordered, ubic.gemma.core.search.SearchSource)
- ubic.gemma.core.loader.util.anndata.Dataframe<K> (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
- ubic.gemma.core.loader.expression.DataLoaderConfig
  - ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig
    - ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig
      - ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig
        
        ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig
      - ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig
- ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder<C,B>
  - ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>
    - ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>
      - ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B>
        
        ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>
      - ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfig.MexSingleCellDataLoaderConfigBuilder<C,B>
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Dataset
- ubic.gemma.core.loader.expression.cellxgene.model.DatasetAsset
- ubic.gemma.core.loader.expression.cellxgene.model.DatasetAssetDownloadMetadata
- ubic.gemma.core.loader.expression.geo.DatasetCombiner
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetDescription
- ubic.gemma.core.loader.expression.cellxgene.model.DatasetMetadata
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.DatasetSummary
- ubic.gemma.core.config.DataSourceConfig
- ubic.gemma.core.loader.expression.DataUpdaterAuditServiceImpl (implements ubic.gemma.core.loader.expression.DataUpdaterAuditService)
- ubic.gemma.core.loader.expression.DataUpdaterImpl (implements ubic.gemma.core.loader.expression.DataUpdater)
- ubic.gemma.core.analysis.stats.DataVectorDescriptive
- ubic.gemma.core.util.DateUtil
- ubic.gemma.core.search.DefaultHighlighter (implements ubic.gemma.core.search.Highlighter, ubic.gemma.core.search.OntologyHighlighter)
- ubic.gemma.core.util.DefaultProgressReporterFactory (implements ubic.gemma.core.util.ProgressReporterFactory)
- org.springframework.security.concurrent.DelegatingSecurityContextExecutor (implements java.util.concurrent.Executor)
  - org.springframework.security.concurrent.DelegatingSecurityContextExecutorService (implements java.util.concurrent.ExecutorService)
    - ubic.gemma.core.security.concurrent.DelegatingSecurityContextExecutorService (implements ubic.gemma.core.util.concurrent.DelegatingExecutorService)
  - org.springframework.security.task.DelegatingSecurityContextTaskExecutor (implements org.springframework.core.task.TaskExecutor)
    - org.springframework.security.task.DelegatingSecurityContextAsyncTaskExecutor (implements org.springframework.core.task.AsyncTaskExecutor)
      - ubic.gemma.core.security.concurrent.DelegatingSecurityContextAsyncTaskExecutor (implements ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor)
      - org.springframework.security.scheduling.DelegatingSecurityContextSchedulingTaskExecutor (implements org.springframework.scheduling.SchedulingTaskExecutor)
        
        ubic.gemma.core.security.concurrent.DelegatingSecurityContextSchedulingTaskExecutor (implements org.springframework.context.ApplicationListener<E>, ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor)
    - ubic.gemma.core.security.concurrent.DelegatingSecurityContextTaskExecutor (implements ubic.gemma.core.util.concurrent.DelegatingTaskExecutor)
- ubic.gemma.core.logging.log4j.DelegatingThreadContextCallable<T> (implements java.util.concurrent.Callable<V>)
- ubic.gemma.core.logging.log4j.DelegatingThreadContextExecutor (implements ubic.gemma.core.util.concurrent.DelegatingExecutor)
- ubic.gemma.core.logging.log4j.DelegatingThreadContextRunnable (implements java.lang.Runnable)
- ubic.gemma.core.logging.log4j.DelegatingThreadContextTaskExecutor (implements ubic.gemma.core.util.concurrent.DelegatingTaskExecutor)
  - ubic.gemma.core.logging.log4j.DelegatingThreadContextAsyncTaskExecutor (implements ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor)
    - ubic.gemma.core.logging.log4j.DelegatingThreadContextSchedulingTaskExecutor (implements ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor)
- ubic.gemma.core.loader.util.anndata.DenseMatrix (implements ubic.gemma.core.loader.util.anndata.Matrix)
- ubic.gemma.persistence.util.DescribableComparator (implements java.util.Comparator<T>)
- ubic.gemma.model.common.DescribableUtils
- ubic.gemma.core.util.math.DescriptiveWithMissing
- ubic.gemma.model.expression.experiment.DesignApplyOutcome (implements java.io.Serializable)
- ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan
- ubic.gemma.persistence.service.expression.experiment.DesignCommitPlan.PendingAssignment
- ubic.gemma.core.util.math.linearmodels.DesignMatrix
- ubic.gemma.model.expression.experiment.DesignPreflightReport (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary (implements java.io.Serializable)
- org.hibernate.dialect.Dialect (implements org.hibernate.exception.spi.ConversionContext, org.hibernate.boot.model.FunctionContributor, org.hibernate.boot.model.TypeContributor)
  - org.hibernate.dialect.H2Dialect
    - ubic.gemma.persistence.hibernate.H2Dialect
  - org.hibernate.dialect.MySQLDialect
    - ubic.gemma.persistence.hibernate.MySQL57InnoDBDialect
- ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis.Factory
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilterResult
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService)
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService)
- ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult.Factory
- ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator (implements java.util.Comparator<T>)
- ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator.Factory
- ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileServiceImpl (implements ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileService)
- ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditService)
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService)
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
- ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject (implements java.io.Serializable)
- ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
- ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
- ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService)
- ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.service.DiffExAnalysisResultSetWriter
- ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils
- ubic.gemma.core.analysis.expression.diff.DiffExGeneWarmupService
- ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService)
- ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult (implements java.io.Serializable)
  - ubic.gemma.persistence.service.analysis.expression.diff.MissingResult
  - ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult
- ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch (implements java.io.Serializable)
- ubic.gemma.core.util.math.Distance
- ubic.gemma.core.util.matrix.DoubleMatrixFactory
- ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObjectUtils
- ubic.gemma.core.util.math.linalg.Dqrsl
- org.hibernate.internal.util.xml.DTDEntityResolver (implements org.xml.sax.EntityResolver, java.io.Serializable)
  - ubic.gemma.persistence.hibernate.XSDEntityResolver
- ubic.gemma.core.util.DummyMailSender (implements org.springframework.beans.factory.InitializingBean, org.springframework.mail.MailSender)
- ubic.gemma.persistence.util.EE2CAclQueryUtils
- ubic.gemma.persistence.persister.EeWriteServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.EeWriteService)
- ubic.gemma.persistence.cache.EhcacheConfig
- ubic.gemma.model.analysis.expression.pca.Eigenvalue.Factory
- ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
- ubic.gemma.core.job.notification.EmailNotificationContext
- ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix (implements ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix<T>)
- ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject (implements java.io.Serializable)
- ubic.gemma.core.loader.util.mapper.EntityMapper.MappingStatistics
- ubic.gemma.core.loader.util.mapper.EntityMapperUtils
- ubic.gemma.persistence.util.EntityUrlBuilder
- ubic.gemma.persistence.util.EntityUrlBuilder.AllEntitiesUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.AllRestEntitiesUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.AllWebEntitiesUrl<T>
- ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentUrl
  - ubic.gemma.persistence.util.EntityUrlBuilder.ExternalEntityUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.OntologyEntityUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.RestEntityUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.WebEntityUrl<U>
    - ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignUrl
    - ubic.gemma.persistence.util.EntityUrlBuilder.ArrayDesignWebUrl
    - ubic.gemma.persistence.util.EntityUrlBuilder.ExperimentalDesignWebUrl
    - ubic.gemma.persistence.util.EntityUrlBuilder.ExpressionExperimentWebUrl
- ubic.gemma.persistence.util.EntityUrlBuilder.EntityUrlChooser
- ubic.gemma.persistence.util.EntityUrlBuilder.SomeEntitiesUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.SomeRestEntitiesUrl<T>
  - ubic.gemma.persistence.util.EntityUrlBuilder.SomeWebEntitiesUrl<T>
- ubic.gemma.core.loader.entrez.EntrezQuery
  - ubic.gemma.core.loader.expression.geo.service.GeoQuery
- ubic.gemma.core.loader.entrez.EntrezUtils
- ubic.gemma.core.loader.entrez.EntrezXmlUtils
- ubic.gemma.core.loader.util.anndata.EnumArray (implements ubic.gemma.core.loader.util.anndata.Array<T>)
- ubic.gemma.core.context.EnvironmentProfiles
- ubic.gemma.core.loader.entrez.EutilFetch
- java.util.EventObject (implements java.io.Serializable)
  - org.springframework.context.ApplicationEvent
    - ubic.gemma.core.security.audit.AuditedEvent
- ubic.gemma.core.util.concurrent.Executors
- ubic.gemma.model.expression.experiment.ExperimentalDesign.Factory
- ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl (implements ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter)
- ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadService)
- ubic.gemma.model.expression.experiment.ExperimentalDesignUtils
- ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.BioMaterialFactorValueAssignment
- ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject.ExperimentalFactorEntry
- ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl (implements ubic.gemma.core.visualization.ExperimentalDesignVisualizationService)
- ubic.gemma.core.datastructure.matrix.io.ExperimentalDesignWriter
- ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
- ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadService)
- ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject (implements java.io.Serializable)
- ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneDiffExStats
- ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject (implements java.io.Serializable)
- ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.ExperimentFactorUtils
- ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
- ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService)
- ubic.gemma.core.analysis.service.ExpressionDataDeleterServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionDataDeleterService)
- ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionDataFileService)
- ubic.gemma.core.analysis.service.ExpressionDataFileUtils
- ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilterUtils
- ubic.gemma.core.visualization.ExpressionDataHeatmap (implements ubic.gemma.core.visualization.Heatmap)
- ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort
- ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixRowElement (implements java.lang.Comparable<T>)
- ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionDataMatrixService)
- ubic.gemma.core.analysis.preprocess.svd.ExpressionDataSVD
- ubic.gemma.core.datastructure.matrix.io.ExpressionDataWriterUtils
- ubic.gemma.model.expression.experiment.ExpressionExperiment.Factory
- ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService)
- ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService)
- ubic.gemma.core.loader.entrez.pubmed.ExpressionExperimentBibRefFinder
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao.Identifiers
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService)
- ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig (implements java.io.Serializable)
- ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterResult
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoService)
- ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService)
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService)
- ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl (implements ubic.gemma.core.analysis.report.ExpressionExperimentReportService, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService)
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
- ubic.gemma.model.analysis.expression.ExpressionExperimentSet.Factory
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper)
- ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.Factory
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService)
- ubic.gemma.model.expression.experiment.ExpressionExperimentSubSetUtils
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditService)
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService)
- ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService)
- ubic.gemma.core.util.runtime.ExtendedRuntime
- ubic.gemma.model.common.description.ExternalDatabase.Factory
- ubic.gemma.persistence.service.common.description.ExternalDatabaseReadServiceImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService)
- ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditServiceImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditService)
- ubic.gemma.model.common.description.ExternalDatabases
- ubic.gemma.core.loader.util.ExternalDatabaseUtils
- ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl (implements ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService)
- ubic.gemma.model.expression.experiment.FactorValue.Factory
- ubic.gemma.persistence.util.FactorValueComparator (implements java.util.Comparator<T>)
- ubic.gemma.persistence.service.expression.experiment.FactorValueDeletionImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion)
- ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionService)
- ubic.gemma.core.ontology.FactorValueOntologyServiceImpl (implements ubic.gemma.core.ontology.FactorValueOntologyService)
- ubic.gemma.core.ontology.FactorValueOntologyUtils
- ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
- ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
- ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueReadService)
- ubic.gemma.model.expression.experiment.FactorValueUtils
- ubic.gemma.persistence.util.FactorValueVector
- ubic.gemma.core.util.locking.FileLockInfo
- ubic.gemma.core.util.runtime.FileLockInfo
- ubic.gemma.core.util.locking.FileLockInfoUtils
- ubic.gemma.core.util.locking.FileLockManagerImpl (implements ubic.gemma.core.util.locking.FileLockManager)
- ubic.gemma.core.util.FileTools
- ubic.gemma.core.util.FileUtils
- ubic.gemma.persistence.util.Filter (implements ubic.gemma.persistence.util.PropertyMapping)
- ubic.gemma.persistence.service.FilteringDao.ConjunctSpec
- ubic.gemma.persistence.util.FilterJpaUtils
- ubic.gemma.persistence.util.FilterQueryUtils
- ubic.gemma.persistence.util.Filters (implements java.lang.Iterable<T>)
- ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
- ubic.gemma.persistence.util.FiltersUtils
- ubic.gemma.core.loader.util.ftp.FTPClientFactoryImpl (implements java.lang.AutoCloseable, ubic.gemma.core.loader.util.ftp.FTPClientFactory)
- ubic.gemma.core.loader.util.ftp.FTPConfig
- ubic.gemma.core.util.concurrent.FutureUtils
- ubic.gemma.persistence.service.expression.experiment.GeeqAuditServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.GeeqAuditService)
- ubic.gemma.core.security.acl.GemmaAclConfiguration
- ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder (implements org.springframework.security.crypto.password.PasswordEncoder)
- ubic.gemma.core.util.GemmaRestApiClientImpl (implements ubic.gemma.core.util.GemmaRestApiClient)
- ubic.gemma.core.loader.util.GenBankUtils
- ubic.gemma.model.genome.Gene.Factory
- ubic.gemma.persistence.service.maintenance.Gene2CsStatus (implements java.io.Serializable)
- ubic.gemma.model.association.Gene2GeneAssociation (implements ubic.gemma.model.common.Identifiable)
- ubic.gemma.model.association.Gene2GOAssociation.Factory
- ubic.gemma.persistence.service.association.Gene2GOAssociationReadServiceImpl (implements ubic.gemma.persistence.service.association.Gene2GOAssociationReadService, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.model.genome.gene.GeneAlias.Factory
- ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis.Factory
- ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult.Factory
- ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject (implements ubic.gemma.core.security.model.SecureValueObject)
- ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl (implements ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService)
- ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl (implements ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService)
- ubic.gemma.model.analysis.sequence.GeneMappingSummary (implements java.io.Serializable)
- ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceImpl (implements ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService)
- ubic.gemma.core.search.source.GeneOntologySearchSource (implements ubic.gemma.core.search.SearchSource)
- ubic.gemma.model.genome.GeneOntologyTermValueObject (implements java.io.Serializable)
- ubic.gemma.core.ontology.providers.GeneOntologyUtils
- ubic.gemma.model.genome.gene.GeneProduct.Factory
- ubic.gemma.persistence.service.genome.gene.GeneProductReadServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneProductReadService)
- ubic.gemma.persistence.service.genome.gene.GeneReadServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneReadService)
- ubic.gemma.model.genome.gene.GeneReferenceValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDao)
- ubic.gemma.core.metrics.binder.GenericExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.loader.expression.singleCell.GenericMetadataSingleCellDataLoaderConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
- ubic.gemma.core.metrics.binder.GenericTaskExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSearchService)
- ubic.gemma.model.genome.gene.GeneSet.Factory
- ubic.gemma.model.genome.gene.GeneSetMember.Factory
- ubic.gemma.persistence.service.genome.gene.GeneSetReadServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetReadService)
- ubic.gemma.core.search.GeneSetSearchImpl (implements ubic.gemma.core.search.GeneSetSearch)
- ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper)
- ubic.gemma.persistence.service.genome.gene.GeneWriteServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneWriteService)
- ubic.gemma.persistence.persister.GenomePersister
- ubic.gemma.core.loader.expression.geo.service.GeoBrowserImpl (implements ubic.gemma.core.loader.expression.geo.service.GeoBrowser)
- ubic.gemma.core.loader.expression.geo.model.GeoChannel
- ubic.gemma.core.loader.expression.geo.GeoCharacteristicKey
- ubic.gemma.core.loader.expression.geo.util.GeoConstants
- ubic.gemma.core.loader.expression.geo.model.GeoContact (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.geo.GeoConverterImpl (implements ubic.gemma.core.loader.expression.geo.GeoConverter)
- ubic.gemma.core.loader.expression.geo.model.GeoData (implements java.io.Serializable)
  - ubic.gemma.core.loader.expression.geo.model.GeoDataset
  - ubic.gemma.core.loader.expression.geo.model.GeoPlatform
  - ubic.gemma.core.loader.expression.geo.model.GeoRecord
  - ubic.gemma.core.loader.expression.geo.model.GeoSample (implements java.lang.Comparable<T>)
  - ubic.gemma.core.loader.expression.geo.model.GeoSeries
  - ubic.gemma.core.loader.expression.geo.model.GeoSubset
- ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator (implements ubic.gemma.core.loader.util.sdo.SourceDomainObjectGenerator)
  - ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal
- ubic.gemma.core.loader.expression.geo.GeoFamilyParser (implements ubic.gemma.core.loader.util.parser.Parser<T>)
- ubic.gemma.core.loader.expression.geo.GeoParseResult
- ubic.gemma.core.geoscrape.GeoRecordMatcher.MatchResult
- ubic.gemma.core.loader.expression.geo.model.GeoReplication
- ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig
- ubic.gemma.core.loader.expression.geo.service.GeoRetrieveConfig.GeoRetrieveConfigBuilder
- ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence (implements java.io.Serializable)
- ubic.gemma.core.geoscrape.GeoScrapeDryRunCandidate
- ubic.gemma.core.geoscrape.GeoScrapeService.DryRunResult
- ubic.gemma.core.geoscrape.GeoScrapeService.ScrapeRequest
- ubic.gemma.core.geoscrape.GeoScrapeServiceImpl (implements ubic.gemma.core.geoscrape.GeoScrapeService)
- ubic.gemma.model.expression.experiment.GeoScrapeWatermark (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig
- ubic.gemma.core.loader.expression.geo.service.GeoService.GeoUpdateConfig.GeoUpdateConfigBuilder
- ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl (implements ubic.gemma.core.loader.expression.geo.service.GeoService, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector (implements ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector, java.lang.AutoCloseable, ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector, ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector)
- ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder
- ubic.gemma.core.loader.expression.geo.GeoSourceMetadataBuilder.ExperimentIdentity
- ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditServiceImpl (implements ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditService)
- ubic.gemma.core.loader.expression.geo.service.GeoUtils
- ubic.gemma.core.loader.expression.geo.model.GeoValues (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.geo.model.GeoVariable
- org.springframework.security.config.annotation.method.configuration.GlobalMethodSecurityConfiguration (implements org.springframework.beans.factory.BeanFactoryAware, org.springframework.context.annotation.ImportAware, org.springframework.beans.factory.SmartInitializingSingleton)
  - ubic.gemma.core.security.MethodSecurityConfig
- ubic.gemma.core.goldenpath.GoldenPath (implements java.lang.AutoCloseable)
  - ubic.gemma.core.goldenpath.GoldenPathQuery
  - ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
- ubic.gemma.core.goldenpath.GoldenPathQueryFactoryImpl (implements ubic.gemma.core.goldenpath.GoldenPathQueryFactory)
- ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactoryImpl (implements ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactory)
- ubic.gemma.core.ontology.GoMetricImpl (implements ubic.gemma.core.ontology.GoMetric)
- ubic.gemma.model.common.auditAndSecurity.GroupAuthority.Factory
- ubic.gemma.core.loader.util.hdf5.H5Attribute (implements java.lang.AutoCloseable)
- ubic.gemma.core.loader.util.hdf5.H5Dataset (implements java.lang.AutoCloseable)
- ubic.gemma.core.loader.util.hdf5.H5Dataset.H5Dataspace (implements java.lang.AutoCloseable)
- ubic.gemma.core.loader.util.hdf5.H5Location
  - ubic.gemma.core.loader.util.hdf5.H5File (implements java.io.Closeable)
  - ubic.gemma.core.loader.util.hdf5.H5Group (implements java.lang.AutoCloseable)
- ubic.gemma.core.loader.util.hdf5.H5Type (implements java.lang.AutoCloseable)
- ubic.gemma.core.loader.util.hdf5.H5Utils
- ubic.gemma.core.metrics.binder.jpa.Hibernate4Metrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics (implements java.lang.AutoCloseable, io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.persistence.hibernate.HibernateConfig
- ubic.gemma.core.search.source.HibernateSearchSource (implements ubic.gemma.core.search.FieldAwareSearchSource)
- ubic.gemma.persistence.hibernate.HibernateSessionFactoryBean (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.persistence.hibernate.HibernateUtils
- ubic.gemma.core.metrics.binder.database.HikariCPMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.util.math.distribution.Histogram
- ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
- ubic.gemma.core.analysis.report.HomeStats
- ubic.gemma.core.analysis.report.HomeStats.AccessionSourceStat
- ubic.gemma.core.analysis.report.HomeStats.AddedInWindow
- ubic.gemma.core.analysis.report.HomeStats.CategoryStat
- ubic.gemma.core.analysis.report.HomeStats.FactorValueCategoryStat
- ubic.gemma.core.analysis.report.HomeStats.PerturbedGeneStat
- ubic.gemma.core.analysis.report.HomeStats.RecentExperiment
- ubic.gemma.core.analysis.report.HomeStats.TaxonStat
- ubic.gemma.core.analysis.report.HomeStats.TermStat
- ubic.gemma.core.analysis.report.HomeStats.TreatmentBucketStat
- ubic.gemma.core.analysis.report.HomeStatsRefresher
- ubic.gemma.core.analysis.report.HomeStatsServiceImpl (implements ubic.gemma.core.analysis.report.HomeStatsService, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneConfig
- ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl (implements ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService)
- ubic.gemma.core.ontology.jena.IAO
- ubic.gemma.persistence.util.IdentifiableUtils
- ubic.gemma.model.common.IdentifiableValueObject<O> (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<C>
    - ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject (implements ubic.gemma.model.common.description.Versioned)
    - ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject (implements ubic.gemma.model.expression.experiment.BioAssaySetValueObject)
      - ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
  - ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
    - ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
    - ubic.gemma.model.expression.experiment.FactorValueValueObject
  - ubic.gemma.model.analysis.AnalysisResultSetValueObject<K,R>
    - ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
  - ubic.gemma.model.analysis.AnalysisResultValueObject<A>
    - ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
  - ubic.gemma.model.analysis.AnalysisValueObject<T>
    - ubic.gemma.model.analysis.CellTypeAssignmentValueObject
    - ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject (implements java.io.Serializable)
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject
  - ubic.gemma.model.common.description.AnnotationValueObject
  - ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
  - ubic.gemma.model.common.description.BibliographicReferenceValueObject
    - ubic.gemma.model.common.description.DatasetPublicationValueObject
  - ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
  - ubic.gemma.model.expression.bioAssay.BioAssayValueObject
  - ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
  - ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
  - ubic.gemma.model.blacklist.BlacklistedValueObject
  - ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
  - ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject
  - ubic.gemma.model.common.description.CharacteristicValueObject (implements java.lang.Comparable<T>)
  - ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
  - ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject
  - ubic.gemma.model.common.description.DatabaseEntryValueObject
  - ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
    - ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
    - ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
      - ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
  - ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject
  - ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
  - ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject (implements java.lang.Comparable<T>, ubic.gemma.core.security.model.SecureValueObject)
    - ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject (implements ubic.gemma.model.common.GemmaSessionBackedValueObject)
      - ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
  - ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject (implements ubic.gemma.model.expression.experiment.BioAssaySetValueObject)
  - ubic.gemma.model.common.description.ExternalDatabaseValueObject (implements java.lang.Comparable<T>, ubic.gemma.model.common.description.Versioned)
  - ubic.gemma.model.expression.experiment.GeeqValueObject
    - ubic.gemma.model.expression.experiment.GeeqAdminValueObject
  - ubic.gemma.model.genome.gene.GeneProductValueObject
  - ubic.gemma.model.genome.gene.GeneSetValueObject (implements ubic.gemma.core.security.model.SecureValueObject)
    - ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject
    - ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject (implements ubic.gemma.model.common.GemmaSessionBackedValueObject)
      - ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
      - ubic.gemma.model.genome.gene.GOGroupValueObject
  - ubic.gemma.model.genome.gene.GeneValueObject (implements java.io.Serializable)
  - ubic.gemma.model.common.measurement.MeasurementValueObject
  - ubic.gemma.model.genome.PhysicalLocationValueObject
  - ubic.gemma.model.analysis.ProtocolValueObject
  - ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
  - ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject
  - ubic.gemma.model.expression.experiment.StatementValueObject (implements java.lang.Comparable<T>)
  - ubic.gemma.model.genome.TaxonValueObject
- ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject (implements java.io.Serializable)
- ubic.gemma.core.search.indexer.IndexerServiceImpl (implements ubic.gemma.core.search.indexer.IndexerService)
- java.io.InputStream (implements java.io.Closeable)
  - java.io.FilterInputStream
    - ubic.gemma.core.util.ProgressInputStream
- ubic.gemma.core.ontology.search.JenaTextOntologySearchService (implements ubic.gemma.core.ontology.search.OntologySearchService)
- ubic.gemma.model.common.auditAndSecurity.JobInfo (implements ubic.gemma.model.common.Identifiable, ubic.gemma.model.common.auditAndSecurity.SecuredNotChild)
- ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
- ubic.gemma.core.pipeline.JobReconciler
- ubic.gemma.core.pipeline.JobSnapshot
- ubic.gemma.core.datastructure.matrix.io.JsonMatrixWriter (implements ubic.gemma.core.datastructure.matrix.io.BulkExpressionDataMatrixWriter)
- com.fasterxml.jackson.databind.JsonSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable)
  - ubic.gemma.core.util.RoundingUtils.SignificantDigitsSerializer
- ubic.gemma.model.common.description.Keyword.Factory
- ubic.gemma.core.util.math.KruskalWallis
- ubic.gemma.core.loader.util.anndata.Layer
- ubic.gemma.core.context.LazyInitByDefaultPostProcessor (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor, org.springframework.core.Ordered)
- ubic.gemma.core.util.math.linearmodels.LeastSquaresFit
- ubic.gemma.core.ontology.lexical.LexicalOntologyIndex (implements java.lang.AutoCloseable)
- ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer (implements ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer)
- ubic.gemma.core.util.math.linearmodels.LinearModelSummaryUtils
- ubic.gemma.core.loader.expression.cellxgene.model.Link
- ubic.gemma.core.util.ListUtils
- ubic.gemma.core.logging.log4j.Log4jConfig
- ubic.gemma.core.security.authentication.LoginDetailsValueObject
- ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.search.lucene.LuceneQueryUtils
- ubic.gemma.core.pipeline.LuigiPipelineScheduler (implements ubic.gemma.core.pipeline.PipelineScheduler)
- ubic.gemma.core.mail.MailEngineImpl (implements ubic.gemma.core.mail.MailEngine)
- ubic.gemma.core.mail.MailServiceImpl (implements ubic.gemma.core.mail.MailService)
- ubic.gemma.core.util.ManifestUtils
- ubic.gemma.core.security.authentication.ManualAuthenticationServiceImpl (implements org.springframework.context.ApplicationEventPublisherAware, ubic.gemma.core.security.authentication.ManualAuthenticationService)
- ubic.gemma.core.loader.util.mapper.MapBasedEntityMapper<T> (implements ubic.gemma.core.loader.util.mapper.EntityMapper<T>)
  - ubic.gemma.core.loader.util.mapper.CellIdOverlapBioAssayMapper (implements ubic.gemma.core.loader.util.mapper.BioAssayMapper)
  - ubic.gemma.core.loader.util.mapper.MapBasedDesignElementMapper (implements ubic.gemma.core.loader.util.mapper.DesignElementMapper)
    - ubic.gemma.core.loader.util.mapper.SimpleDesignElementMapper
- ubic.gemma.core.loader.util.anndata.Mapping (implements java.lang.AutoCloseable)
- ubic.gemma.core.util.MarkdownUtils
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.Marker
- ubic.gemma.core.util.math.MathUtil
- ubic.gemma.core.loader.util.MatrixMarketUtils
- ubic.gemma.core.util.math.MatrixNormalizer<R,C>
- ubic.gemma.core.util.math.MatrixRowStats
- ubic.gemma.core.util.math.MatrixStats
- ubic.gemma.core.util.MatrixStats
- ubic.gemma.core.util.matrix.MatrixUtil
- ubic.gemma.core.datastructure.matrix.io.MatrixWriter (implements ubic.gemma.core.datastructure.matrix.io.BulkExpressionDataMatrixWriter)
- ubic.gemma.core.util.matrix.MatrixWriter<R,C>
- ubic.gemma.core.util.math.linearmodels.MeanVarianceEstimator
- ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
- ubic.gemma.core.analysis.preprocess.MeanVarianceServiceImpl (implements ubic.gemma.core.analysis.preprocess.MeanVarianceService)
- ubic.gemma.core.datastructure.matrix.io.MeanVarianceWriter
- ubic.gemma.model.common.measurement.Measurement.Factory
- ubic.gemma.model.common.measurement.MeasurementUtils
- ubic.gemma.model.common.description.MedicalSubjectHeading.Factory
- ubic.gemma.persistence.util.MessagesConfig
- ubic.gemma.core.util.math.metaanalysis.MetaAnalysis
  - ubic.gemma.core.util.math.metaanalysis.CorrelationEffectMetaAnalysis
  - ubic.gemma.core.util.math.metaanalysis.MeanDifferenceMetaAnalysis
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaField
- org.springframework.util.MethodInvoker
  - org.springframework.beans.support.ArgumentConvertingMethodInvoker
    - org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean (implements org.springframework.beans.factory.BeanClassLoaderAware, org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean)
      - ubic.gemma.core.scheduler.SecureMethodInvokingJobDetailFactoryBean
- ubic.gemma.core.config.MetricsConfig
- ubic.gemma.core.datastructure.matrix.io.MexMatrixBundler
- ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter (implements ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter)
- ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoader (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader)
- ubic.gemma.core.ontology.relation.MgiRelationProducer
- ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.pipeline.MockPipelineScheduler (implements ubic.gemma.core.pipeline.PipelineScheduler)
- ubic.gemma.model.util.ModelUtils
- ubic.gemma.core.util.math.linearmodels.ModeratedTstat
- ubic.gemma.core.ontology.providers.mondo.MondoSeedResolver
- ubic.gemma.model.genome.gene.Multifunctionality.Factory
- ubic.gemma.core.util.math.MultipleTestCorrection
- ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGene2Accession
- ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader
- ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter (implements ubic.gemma.core.loader.util.converter.Converter<S,T>)
- ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneData
- ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator
- ubic.gemma.core.loader.genome.gene.ncbi.model.NcbiGeneHistory
- ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
- ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneLoader
- ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneUtils
- ubic.gemma.core.util.NetDatasourceUtil
  - ubic.gemma.core.loader.expression.arrayExpress.util.ArrayExpressUtil
  - ubic.gemma.core.loader.expression.geo.util.GeoUtil
  - ubic.gemma.core.loader.genome.gene.ncbi.NCBIUtil
- ubic.gemma.core.util.NetUtils
- ubic.gemma.core.pipeline.NextflowPipelineScheduler (implements ubic.gemma.core.pipeline.PipelineScheduler)
- ubic.gemma.core.loader.util.anndata.NullableArray<T> (implements ubic.gemma.core.loader.util.anndata.Array<T>, java.lang.AutoCloseable)
  - ubic.gemma.core.loader.util.anndata.NullableBoolArray
  - ubic.gemma.core.loader.util.anndata.NullableIntArray
- ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader)
- ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoaderConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
- ubic.gemma.core.security.acl.ObjectIdentityRetrievalStrategyImpl (implements org.springframework.security.acls.model.ObjectIdentityRetrievalStrategy)
- ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategyImpl (implements ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategy)
- ubic.gemma.core.ontology.ObsoleteTermCorrectionResult (implements java.io.Serializable)
- ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync (implements java.io.Serializable)
- ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection (implements java.io.Serializable)
- ubic.gemma.core.ontology.ObsoleteTermCorrectionServiceImpl (implements ubic.gemma.core.ontology.ObsoleteTermCorrectionService)
- ubic.gemma.core.ontology.ObsoleteTermUsage (implements java.io.Serializable)
- ubic.gemma.core.ontology.ols.OlsTerm (implements java.io.Serializable)
- ubic.gemma.core.ontology.ols.OlsTermResolverImpl (implements ubic.gemma.core.ontology.ols.OlsTermResolver)
- ubic.gemma.core.ontology.search.OntologyAnalyzers
- ubic.gemma.core.ontology.OntologyConfig
- ubic.gemma.core.ontology.OntologyExternalLinks
- ubic.gemma.core.ontology.jena.OntologyLoader
- ubic.gemma.core.ontology.search.OntologyQueries
- ubic.gemma.core.ontology.relation.OntologyRelationProducerImpl (implements ubic.gemma.core.ontology.relation.OntologyRelationProducer)
- ubic.gemma.core.ontology.search.OntologySearchResult<T> (implements java.util.Comparator<T>)
- ubic.gemma.core.ontology.search.OntologySearchService.Result
- ubic.gemma.core.search.source.OntologySearchSource (implements ubic.gemma.core.search.SearchSource)
- ubic.gemma.core.ontology.OntologyServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.ontology.OntologyService)
- ubic.gemma.core.ontology.providers.OntologyServiceResolver
- ubic.gemma.core.ontology.providers.OntologySlimExtractor
- ubic.gemma.core.ontology.providers.OntologySlimExtractor.ExtractResult
- ubic.gemma.core.ontology.providers.OntologySlimMeta
- ubic.gemma.core.ontology.simple.OntologyStatementSimple (implements ubic.gemma.core.ontology.model.OntologyStatement)
- ubic.gemma.core.loader.expression.cellxgene.model.OntologyTerm
- ubic.gemma.core.ontology.model.OntologyTerm.TaxonConstraint
- ubic.gemma.core.ontology.OntologyTermValidatorImpl (implements ubic.gemma.core.ontology.OntologyTermValidator)
- ubic.gemma.core.ontology.OntologyUtils
- ubic.gemma.core.ontology.model.OntologyXref
- ubic.gemma.core.ontology.relation.OntologyXrefIndex
- ubic.gemma.core.analysis.preprocess.OutlierDetails (implements java.io.Serializable)
- ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl (implements ubic.gemma.core.analysis.preprocess.OutlierDetectionService)
- ubic.gemma.core.analysis.service.OutlierFlaggingAuditServiceImpl (implements ubic.gemma.core.analysis.service.OutlierFlaggingAuditService)
- ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl (implements ubic.gemma.core.analysis.service.OutlierFlaggingService)
- ubic.gemma.core.analysis.preprocess.filter.OutliersFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategyImpl (implements ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategy)
- ubic.gemma.core.loader.util.ParserAndLoaderTools
- cern.colt.PersistentObject (implements java.lang.Cloneable, java.io.Serializable)
  - cern.colt.matrix.impl.AbstractMatrix
    - cern.colt.matrix.impl.AbstractMatrix1D
      - cern.colt.matrix.DoubleMatrix1D
        
        cern.colt.matrix.impl.DenseDoubleMatrix1D
        
        ubic.gemma.core.util.matrix.DenseDoubleMatrix1D
- ubic.gemma.persistence.persister.PersisterHelperImpl (implements ubic.gemma.persistence.persister.PersisterHelper)
- ubic.gemma.model.genome.PhysicalLocation.Factory
- ubic.gemma.persistence.service.pipeline.PipelineJobBatchServiceImpl (implements ubic.gemma.persistence.service.pipeline.PipelineJobBatchService)
- ubic.gemma.persistence.util.Pointcuts
- ubic.gemma.persistence.service.expression.experiment.PreboardedAuditServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.PreboardedAuditService)
- ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PromotionResult
- ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService)
- ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
- ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.PreprocessorHelperService)
- ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl (implements ubic.gemma.core.analysis.preprocess.PreprocessorService)
- ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis.Factory
- ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadService)
- ubic.gemma.model.analysis.expression.pca.ProbeLoading.Factory
- ubic.gemma.core.analysis.sequence.ProbeMapperConfig
- ubic.gemma.core.analysis.sequence.ProbeMapperImpl (implements ubic.gemma.core.analysis.sequence.ProbeMapper)
- ubic.gemma.core.analysis.sequence.ProbeMapUtils
- ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector.Factory
- ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditService)
- ubic.gemma.core.profiling.ProfilingConfig
- ubic.gemma.core.job.progress.ProgressData (implements java.io.Serializable)
- ubic.gemma.core.logging.log4j.ProgressUpdateAppender.ProgressUpdateContextImpl (implements ubic.gemma.core.job.progress.ProgressUpdateContext)
- ubic.gemma.persistence.util.PropertyMappingUtils
- ubic.gemma.model.common.protocol.Protocol.Factory
- ubic.gemma.persistence.service.common.protocol.ProtocolReadServiceImpl (implements ubic.gemma.persistence.service.common.protocol.ProtocolReadService)
- ubic.gemma.persistence.service.common.description.PublicationAssertion
- ubic.gemma.persistence.service.common.description.PublicationAssociationServiceImpl (implements ubic.gemma.persistence.service.common.description.PublicationAssociationService)
- ubic.gemma.model.common.description.PublicationAssociationValueObject
- ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
- ubic.gemma.core.loader.entrez.pubmed.PubMedService
- ubic.gemma.core.loader.entrez.pubmed.PubMedUtils
- ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
- ubic.gemma.model.analysis.expression.diff.PvalueDistribution.Factory
- ubic.gemma.core.util.math.linalg.QRDecomposition
- ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer<R,C>
- ubic.gemma.model.common.quantitationtype.QuantitationType.Factory
- ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionUtils
- ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionUtils
- ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
- ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadServiceImpl (implements ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService)
- ubic.gemma.model.common.quantitationtype.QuantitationTypeUtils
- org.springframework.scheduling.quartz.QuartzJobBean (implements org.quartz.Job)
  - ubic.gemma.core.scheduler.SecureQuartzJobBean
    - ubic.gemma.core.scheduler.BatchInfoRepopulationJob (implements org.quartz.StatefulJob)
    - ubic.gemma.core.scheduler.Ee2AdUpdateJob (implements org.quartz.StatefulJob)
    - ubic.gemma.core.scheduler.Ee2cUpdateJob (implements org.quartz.StatefulJob)
- ubic.gemma.persistence.util.QueryUtils
- ubic.gemma.model.analysis.expression.diff.RandomDifferentialExpressionAnalysisUtils
- ubic.gemma.core.util.math.Rank
- ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector.Factory
- ubic.gemma.core.loader.util.parser.RecordParser<T> (implements ubic.gemma.core.loader.util.parser.Parser<T>)
  - ubic.gemma.core.loader.genome.FastaParser
  - ubic.gemma.core.loader.genome.gene.SwissProtParser
- ubic.gemma.model.association.ReferenceAssociation.Factory
- ubic.gemma.persistence.persister.RelationshipPersister
- ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapper (implements ubic.gemma.core.loader.util.mapper.BioAssayMapper)
- ubic.gemma.core.loader.util.mapper.RenamingBioAssayMapperParser
- ubic.gemma.core.analysis.sequence.RepeatScan
- ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
- ubic.gemma.core.analysis.preprocess.convert.RepresentationConversionUtils
- ubic.gemma.core.util.ResourceUtils
- ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.retry.RetryLogger (implements org.springframework.retry.RetryListener)
- ubic.gemma.core.ontology.jena.RO
- ubic.gemma.core.util.RoundingUtils
- ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis.Factory
- ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService)
- ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditService)
- ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix.Factory
- ubic.gemma.core.analysis.preprocess.convert.ScaleTypeConversionUtils
- ubic.gemma.core.search.indexer.ScheduledSearchReindexer
- ubic.gemma.core.config.SchedulerConfig
- ubic.gemma.core.pipeline.SchedulerHandle
- ubic.gemma.core.search.SearchContext
- ubic.gemma.model.common.search.SearchResult<T> (implements java.lang.Comparable<T>)
- ubic.gemma.core.search.SearchResultDisplayObject (implements java.lang.Comparable<T>)
- ubic.gemma.model.common.search.SearchResultValueObject<T>
- ubic.gemma.core.search.SearchServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.search.SearchService)
- ubic.gemma.model.common.search.SearchSettings
- ubic.gemma.model.common.search.SearchSettings.SearchSettingsBuilder
- ubic.gemma.model.common.search.SearchSettingsValueObject (implements java.io.Serializable)
- ubic.gemma.core.security.SecurityConfig
- ubic.gemma.core.security.SecurityServiceImpl (implements ubic.gemma.core.security.SecurityService)
- ubic.gemma.core.security.util.SecurityUtil
- ubic.gemma.persistence.util.SecurityUtils
- ubic.gemma.core.config.SentinelPropertyValidator (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.analysis.sequence.SequenceBinUtils
- ubic.gemma.core.analysis.sequence.SequenceManipulation
- ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.sequence.SequenceWriter
- ubic.gemma.core.loader.expression.sequencing.SequencingMetadata
- ubic.gemma.core.loader.expression.sequencing.SequencingMetadata.SequencingMetadataBuilder
- ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoaderConfigurer (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>)
- ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics
- ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.MetricDefinition
- ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.RunMetrics
- ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetrics.SampleMetrics
- ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsServiceImpl (implements ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsService)
- ubic.gemma.persistence.util.ServiceBasedEntityConverter<O> (implements org.springframework.core.convert.converter.ConditionalGenericConverter)
  - ubic.gemma.persistence.util.ServiceBasedValueObjectConverter<O,VO> (implements org.springframework.core.convert.converter.ConditionalGenericConverter)
- ubic.gemma.core.config.ServiceBeansConfig
- ubic.gemma.core.config.Settings
- ubic.gemma.core.config.SettingsConfig
- ubic.gemma.core.analysis.sequence.ShellDelegatingBlat (implements ubic.gemma.core.analysis.sequence.Blat)
- ubic.gemma.core.util.ShellUtils
- ubic.gemma.core.security.acl.domain.Sids
- ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry (implements java.io.Serializable)
- ubic.gemma.core.util.SimpleDownloader
- ubic.gemma.core.util.SimpleDownloader.URLAndDestination
- ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService)
- ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata (implements java.io.Serializable)
- ubic.gemma.core.loader.genome.SimpleFastaCmd (implements ubic.gemma.core.loader.genome.FastaCmd)
- ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata (implements java.io.Serializable)
- ubic.gemma.core.util.SimpleRetry<E>
- ubic.gemma.core.util.SimpleRetryContext
- ubic.gemma.core.util.SimpleRetryPolicy
- ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata (implements java.io.Serializable)
- ubic.gemma.core.util.concurrent.SimpleThreadFactory (implements java.util.concurrent.ThreadFactory)
- org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler (implements org.springframework.security.web.authentication.AuthenticationFailureHandler)
  - ubic.gemma.core.security.authentication.AjaxAuthenticationFailureHandler
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationConfig.SingleCellAggregationConfigBuilder
- ubic.gemma.core.geoscrape.SingleCellBrainMatcher (implements ubic.gemma.core.geoscrape.GeoRecordMatcher)
- ubic.gemma.core.visualization.SingleCellDataBoxplot
- ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderServiceImpl (implements ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService)
- ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactoryImpl (implements ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactory)
- ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationPipeline (implements ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation, ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformation, ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation)
- ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationUtils
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils
- ubic.gemma.core.analysis.singleCell.SingleCellDescriptive
- ubic.gemma.model.expression.bioAssayData.SingleCellDimensionUtils
- ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditService)
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExperimentSubSetsCreationConfig.SingleCellExperimentSubSetsCreationConfigBuilder
- ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrixUtils
- ubic.gemma.model.expression.bioAssayData.SingleCellExpressionDataVectorUtils
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditServiceImpl (implements ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditService)
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl (implements ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService)
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl (implements ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService)
- ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
- ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig.SingleCellDimensionInitializationConfigBuilder
- ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig
- ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig.SingleCellVectorInitializationConfigBuilder
- ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService)
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditServiceImpl (implements ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditService)
- ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetServiceImpl (implements ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetService)
- ubic.gemma.core.analysis.singleCell.SingleCellMaskUtils
- ubic.gemma.core.analysis.singleCell.SingleCellSlicerUtils
- ubic.gemma.core.visualization.SingleCellSparsityHeatmap (implements ubic.gemma.core.visualization.Heatmap)
- ubic.gemma.core.analysis.singleCell.SingleCellSparsityMetrics
- ubic.gemma.core.loader.expression.singleCell.transform.SingleCellTransformationConfig
- ubic.gemma.core.util.math.linalg.SingularValueDecomposition<R,C>
- ubic.gemma.core.util.math.Smooth
- ubic.gemma.persistence.util.Sort (implements ubic.gemma.persistence.util.PropertyMapping)
- ubic.gemma.core.datastructure.sparse.SparseListUtils
- ubic.gemma.core.loader.util.anndata.SparseMatrix (implements ubic.gemma.core.loader.util.anndata.Matrix)
- ubic.gemma.core.util.math.SpecFunc
- ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl (implements ubic.gemma.core.analysis.preprocess.SplitExperimentService)
- ubic.gemma.core.context.SpringContextUtils
- ubic.gemma.core.util.SQLUtils
- ubic.gemma.core.loader.expression.sra.model.SraBase
- ubic.gemma.core.loader.expression.sra.model.SraBases
- ubic.gemma.core.loader.expression.sra.model.SraContact
- ubic.gemma.core.loader.expression.sra.model.SraExperiment
- ubic.gemma.core.loader.expression.sra.model.SraExperimentDesign
- ubic.gemma.core.loader.expression.sra.model.SraExperimentPackage
- ubic.gemma.core.loader.expression.sra.model.SraExperimentPackageSet
- ubic.gemma.core.loader.expression.sra.model.SraExternalId
- ubic.gemma.core.loader.expression.sra.SraFetcher
- ubic.gemma.core.loader.expression.sra.model.SraFile
- ubic.gemma.core.loader.expression.sra.model.SraFiles
- ubic.gemma.core.loader.expression.sra.model.SraIdentifiers
- ubic.gemma.core.loader.expression.sra.model.SraLibraryDescriptor
- ubic.gemma.core.loader.expression.sra.model.SraLibraryLayout
- ubic.gemma.core.loader.expression.sra.model.SraOrganization
- ubic.gemma.core.loader.expression.sra.model.SraPlatform
- ubic.gemma.core.loader.expression.sra.model.SraPool
- ubic.gemma.core.loader.expression.sra.model.SraPoolMember
- ubic.gemma.core.loader.expression.sra.model.SraPrimaryId
- ubic.gemma.core.loader.expression.sra.model.SraReadStatistics
- ubic.gemma.core.loader.expression.sra.model.SraRun
- ubic.gemma.core.loader.expression.sra.SraRuninfoParser
- ubic.gemma.core.loader.expression.sra.model.SraRunSet
- ubic.gemma.core.loader.expression.sra.model.SraRunStatistics
- ubic.gemma.core.loader.expression.sra.model.SraSubmission
- ubic.gemma.core.loader.expression.sra.model.SraSubmitterId
- ubic.gemma.core.loader.expression.sra.SraUtils
- ubic.gemma.core.loader.expression.sra.SraXmlParser
- ubic.gemma.model.expression.experiment.Statement.Factory
- ubic.gemma.model.expression.experiment.StatementUtils
- ubic.gemma.persistence.cache.StaticCacheKeyLock (implements ubic.gemma.persistence.cache.CacheKeyLock)
- ubic.gemma.core.util.math.Stats
- com.fasterxml.jackson.databind.util.StdConverter<IN,OUT> (implements com.fasterxml.jackson.databind.util.Converter<IN,OUT>)
  - ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject.FromArrayDesignValueObject
- ubic.gemma.core.profiling.StopWatchUtils
- ubic.gemma.core.profiling.StopWatchUtils.StopWatchRegion (implements java.lang.AutoCloseable)
- ubic.gemma.core.util.math.StringDistance
- ubic.gemma.core.util.StringUtil
- ubic.gemma.core.util.StringUtils
- ubic.gemma.core.pipeline.SubmitRequest
- ubic.gemma.core.job.SubmittedTasksMaintenance
- ubic.gemma.persistence.util.Subquery
- ubic.gemma.persistence.util.Subquery.Alias
- ubic.gemma.persistence.util.SubqueryUtils
- ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException.SuspiciousValueResult
- ubic.gemma.core.analysis.preprocess.svd.SVDResult
- ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl (implements ubic.gemma.core.analysis.preprocess.svd.SVDService)
- ubic.gemma.core.util.SymbolFontPua
- ubic.gemma.core.loader.expression.synapse.SynapseUtils
- ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl (implements ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil)
- ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter (implements ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter)
- ubic.gemma.core.job.TaskCommand (implements java.io.Serializable)
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
  - ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
  - ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
  - ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
    - ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
  - ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
  - ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
  - ubic.gemma.core.tasks.EntityTaskCommand<T>
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand
  - ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
    - ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand
  - ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand
  - ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
  - ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand
  - ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand
  - ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand
- ubic.gemma.core.security.concurrent.TaskExecutorConfig
- ubic.gemma.core.security.concurrent.TaskExecutorSecurityContextDelegatePostProcessor (implements org.springframework.beans.factory.config.BeanPostProcessor)
- ubic.gemma.core.logging.log4j.TaskExecutorThreadContextInheritPostProcessor (implements org.springframework.beans.factory.config.BeanPostProcessor)
- ubic.gemma.core.job.notification.TaskMailUtilsImpl (implements ubic.gemma.core.job.notification.TaskMailUtils)
- ubic.gemma.core.job.notification.TaskPostProcessingImpl (implements ubic.gemma.core.job.notification.TaskPostProcessing)
- ubic.gemma.core.job.TaskResult (implements java.io.Serializable)
- ubic.gemma.core.job.TaskRunningServiceImpl (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.InitializingBean, ubic.gemma.core.job.TaskRunningService)
- ubic.gemma.model.genome.Taxon.Factory
- ubic.gemma.core.loader.genome.taxon.TaxonLoader
- ubic.gemma.persistence.service.genome.taxon.TaxonReadServiceImpl (implements ubic.gemma.persistence.service.genome.taxon.TaxonReadService)
- ubic.gemma.persistence.service.genome.taxon.TaxonUtils
- ubic.gemma.core.loader.expression.singleCell.TenXCellRangerUtils
- ubic.gemma.core.ontology.TermCanonicalization
- ubic.gemma.core.ontology.TermViolation
- ubic.gemma.persistence.initialization.TestBootstrapState
- ubic.gemma.core.geoscrape.TfPerturbationMatcher (implements ubic.gemma.core.geoscrape.GeoRecordMatcher)
- ubic.gemma.core.ontology.jena.TGFVO
- ubic.gemma.persistence.util.Thaws
- ubic.gemma.core.metrics.binder.ThreadPoolExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.util.concurrent.ThreadUtils
- java.lang.Throwable (implements java.io.Serializable)
  - java.lang.Exception
    - ubic.gemma.core.analysis.preprocess.filter.FilteringException
      - ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException
        
        ubic.gemma.core.analysis.preprocess.filter.InsufficientDesignElementsException
        
        ubic.gemma.core.analysis.preprocess.filter.NoDesignElementsException
        
        ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException
        
        ubic.gemma.core.analysis.preprocess.filter.NoSamplesException
    - java.io.IOException
      - ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException
    - ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException
    - ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException
    - ubic.gemma.core.ontology.ols.OlsUnavailableException
    - ubic.gemma.core.ontology.search.OntologySearchException
    - ubic.gemma.core.pipeline.PipelineSchedulerException
    - ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException
    - ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PreboardedAlreadyPromotedException
    - ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException
      - ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationTypeConversionException
        
        ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationRepresentationConversionException
        
        ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException
    - ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException
      - ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException
        
        ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException
        
        ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException
    - java.lang.RuntimeException
      - ubic.gemma.core.loader.util.AlreadyExistsInSystemException
      - ubic.gemma.core.analysis.expression.diff.AnalysisException
        
        ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException
        
        ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException
        
        ubic.gemma.core.analysis.expression.diff.EbayesFailureException
        
        ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException
        
        ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException
        
        ubic.gemma.core.analysis.expression.diff.MeanVarianceFailureException
        
        ubic.gemma.core.analysis.expression.diff.MultipleBaselinesRequireSubsetException
        
        ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException
      - ubic.gemma.core.loader.util.anndata.AnnDataException
        
        ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException
        
        ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException
      - ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException
      - ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException
      - ubic.gemma.core.loader.entrez.EntrezException
      - ubic.gemma.core.loader.util.parser.FileFormatException
      - ubic.gemma.core.util.GemmaRestApiClientException
      - ubic.gemma.core.loader.util.hdf5.H5Exception
      - java.lang.IllegalArgumentException
        
        ubic.gemma.model.common.NonUniqueDescribableByNameException
        
        ubic.gemma.core.loader.expression.singleCell.NonUniqueCellLevelCharacteristicsByNameException
        
        ubic.gemma.core.loader.expression.singleCell.NonUniqueCellTypeAssignmentByNameException
        
        ubic.gemma.persistence.service.common.description.PublicationAssociationConflictException
      - ubic.gemma.core.analysis.preprocess.PreprocessingException
        
        ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
        
        ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException
        
        ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException
        
        ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException
        
        ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException
        
        ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
      - ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationException
        
        ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForSingleCellAggregationException
      - ubic.gemma.model.util.UninitializedCollectionException
      - ubic.gemma.persistence.util.UnsupportedEntityUrlException
    - ubic.gemma.core.search.SearchException
      - ubic.gemma.core.search.BaseCodeOntologySearchException
      - ubic.gemma.core.search.source.HibernateSearchException
      - ubic.gemma.core.search.ParseSearchException
        
        ubic.gemma.core.search.lucene.LuceneParseSearchException
      - ubic.gemma.core.search.SearchTimeoutException
    - ubic.gemma.core.analysis.preprocess.svd.SVDException
    - ubic.gemma.core.security.authentication.UserExistsException
- ubic.gemma.model.common.auditAndSecurity.curation.Ticket.Factory
- ubic.gemma.model.common.auditAndSecurity.curation.TicketEvent.Factory
- ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject (implements java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject (implements java.io.Serializable)
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService.TargetAddition
- ubic.gemma.model.common.auditAndSecurity.curation.TicketTarget.Factory
- ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject (implements java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.preprocess.filter.TooFewDistinctValuesFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)
- ubic.gemma.core.visualization.TransposedHeatMapDataset (implements org.jfree.data.general.HeatMapDataset)
- ubic.gemma.model.expression.biomaterial.Treatment.Factory
- ubic.gemma.core.analysis.report.TreatmentBucketsConfig
- ubic.gemma.core.analysis.report.TreatmentBucketsConfig.Bucket
- ubic.gemma.core.util.TsvUtils
- ubic.gemma.core.datastructure.matrix.TwoChannelExpressionDataMatrixBuilder
- ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl (implements ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues)
- ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils
- ubic.gemma.model.util.UninitializedCollection<T> (implements java.util.Collection<E>)
  - ubic.gemma.model.util.UninitializedList<T> (implements java.util.List<E>)
  - ubic.gemma.model.util.UninitializedSet<T> (implements java.util.Set<E>)
- ubic.gemma.model.common.measurement.Unit.Factory
- ubic.gemma.model.common.auditAndSecurity.User.Factory
- ubic.gemma.core.security.authentication.UserDetailsImpl (implements org.springframework.security.core.userdetails.UserDetails)
- ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
- ubic.gemma.core.security.authentication.UserManagerImpl (implements org.springframework.security.core.userdetails.UserDetailsPasswordService, ubic.gemma.core.security.authentication.UserManager)
- ubic.gemma.core.security.authentication.UserReadServiceImpl (implements ubic.gemma.core.security.authentication.UserReadService)
- ubic.gemma.core.security.authentication.UserServiceImpl (implements org.springframework.context.ApplicationContextAware, ubic.gemma.core.security.authentication.UserService)
- ubic.gemma.core.util.graphics.text.Util
- ubic.gemma.model.common.description.Value
- ubic.gemma.persistence.util.ValueObjectConfig
- ubic.gemma.model.common.description.Values
- ubic.gemma.core.ontology.ValueStringToOntologyMapping
- ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl (implements ubic.gemma.core.analysis.preprocess.VectorMergingService)
- ubic.gemma.core.mail.VelocityConfig
- ubic.gemma.core.metrics.binder.VirtualThreadExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
- ubic.gemma.core.analysis.report.WhatsNew
- ubic.gemma.core.analysis.report.WhatsNewServiceImpl (implements ubic.gemma.core.analysis.report.WhatsNewService)
- ubic.gemma.persistence.service.expression.experiment.WorkflowQueueEntry
- ubic.gemma.persistence.service.expression.experiment.WorkflowServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.WorkflowService)
- ubic.gemma.persistence.service.expression.experiment.WorkflowTransition
- jakarta.xml.bind.annotation.adapters.XmlAdapter<ValueType, BoundType>
  - ubic.gemma.core.loader.expression.sra.model.SraDateParser
- ubic.gemma.core.util.XMLUtils
- ubic.gemma.core.loader.expression.zenodo.ZenodoUtils
- ubic.gemma.core.analysis.preprocess.filter.ZeroVarianceFilter (implements ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>)

Interface Hierarchy

ubic.gemma.core.security.acl.domain.AclDao
ubic.gemma.core.security.authorization.acl.AclLinterHelperService
ubic.gemma.core.security.authorization.acl.AclLinterService
org.springframework.security.acls.model.AclService
- org.springframework.security.acls.model.MutableAclService
  - ubic.gemma.core.security.acl.domain.AclService
ubic.gemma.core.analysis.expression.AnalysisUtilService
ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationReadService
ubic.gemma.persistence.service.common.description.AnnotationRelationService
ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionService
ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService
ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageService
ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeAuditService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadService
ubic.gemma.core.analysis.report.ArrayDesignReportService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
ubic.gemma.core.security.audit.AuditEventPayload
ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
java.lang.AutoCloseable
- ubic.gemma.core.security.util.ActingIdentity.Scope
- ubic.gemma.core.loader.util.anndata.Array<T>
- ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition
- java.io.Closeable
  - ubic.gemma.core.loader.expression.DataLoader
    - ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader
      - ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader (also extends ubic.gemma.core.loader.expression.DataLoader)
    - ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader (also extends ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader)
- java.util.concurrent.ExecutorService (also extends java.util.concurrent.Executor)
  - ubic.gemma.core.util.concurrent.DelegatingExecutorService (also extends ubic.gemma.core.util.concurrent.DelegatingExecutor)
    - ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService (also extends java.util.concurrent.ScheduledExecutorService)
  - java.util.concurrent.ScheduledExecutorService
    - ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService (also extends ubic.gemma.core.util.concurrent.DelegatingExecutorService)
- ubic.gemma.core.util.locking.LockedPath
- ubic.gemma.core.loader.util.anndata.Matrix
- ubic.gemma.core.ontology.providers.OntologyService
  - ubic.gemma.core.ontology.providers.GeneOntologyService
  - ubic.gemma.core.ontology.providers.SlimmableOntologyService
- ubic.gemma.core.util.ProgressReporter
- ubic.gemma.core.job.progress.ProgressUpdateContext
ubic.gemma.persistence.service.BaseDao<T>
- ubic.gemma.persistence.service.analysis.AnalysisDao<T>
  - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
- ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>
  - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
- ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
- ubic.gemma.persistence.service.common.description.AnnotationRelationDao
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDispositionDao
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageDao
- ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
- ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao
- ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>
  - ubic.gemma.persistence.service.common.description.BibliographicReferenceDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
  - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDao
  - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
  - ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
  - ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
  - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao
  - ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
  - ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.FilteringDao<O>)
    - ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
    - ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.CachedFilteringDao<O>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
    - ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
    - ubic.gemma.persistence.service.common.description.DatabaseEntryDao
    - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>)
    - ubic.gemma.persistence.service.expression.experiment.FactorValueDao
    - ubic.gemma.persistence.service.genome.GeneDao
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
    - ubic.gemma.persistence.service.genome.taxon.TaxonDao
  - ubic.gemma.persistence.service.expression.experiment.GeeqDao
  - ubic.gemma.persistence.service.genome.gene.GeneProductDao
  - ubic.gemma.persistence.service.genome.gene.GeneSetDao
- ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
- ubic.gemma.persistence.service.BrowsingDao<T>
  - ubic.gemma.persistence.service.common.description.BibliographicReferenceDao (also extends ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
  - ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
- ubic.gemma.persistence.service.genome.ChromosomeDao
- ubic.gemma.persistence.service.expression.biomaterial.CompoundDao
- ubic.gemma.persistence.service.common.auditAndSecurity.ContactDao
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionDao
- ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao<T>
  - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
  - ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDao
  - ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
- ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
- ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
- ubic.gemma.persistence.service.FilteringDao<O>
  - ubic.gemma.persistence.service.CachedFilteringDao<O>
    - ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
  - ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
    - ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
    - ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.CachedFilteringDao<O>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
    - ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
    - ubic.gemma.persistence.service.common.description.DatabaseEntryDao
    - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>)
    - ubic.gemma.persistence.service.expression.experiment.FactorValueDao
    - ubic.gemma.persistence.service.genome.GeneDao
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
    - ubic.gemma.persistence.service.genome.taxon.TaxonDao
- ubic.gemma.persistence.service.association.Gene2GOAssociationDao
- ubic.gemma.persistence.service.genome.gene.GeneAliasDao
- ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
- ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao
- ubic.gemma.persistence.service.pipeline.PipelineJobBatchDao
- ubic.gemma.persistence.service.pipeline.PipelineJobDao
- ubic.gemma.persistence.service.pipeline.PipelineJobEventDao
- ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
- ubic.gemma.persistence.service.common.protocol.ProtocolDao
- ubic.gemma.persistence.service.common.description.PublicationAssociationDao
- ubic.gemma.persistence.service.association.ReferenceAssociationDao
- ubic.gemma.persistence.service.expression.experiment.SingleCellDimensionExperimentDao
- ubic.gemma.persistence.service.expression.experiment.StatementDao
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketDao
- ubic.gemma.persistence.service.common.measurement.UnitDao
- ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
- ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
ubic.gemma.persistence.service.BaseReadOnlyService<O>
- ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>
  - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
- ubic.gemma.persistence.service.BaseImmutableService<O>
  - ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService<O>
    - ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
    - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
  - ubic.gemma.persistence.service.analysis.AnalysisService<T>
    - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
  - ubic.gemma.persistence.service.BaseService<O>
    - ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>
      - ubic.gemma.persistence.service.genome.biosequence.BioSequenceService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      - ubic.gemma.persistence.service.genome.gene.GeneProductService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      - ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.description.BibliographicReferenceService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
    - ubic.gemma.persistence.service.common.description.ExternalDatabaseService
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService<C>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.curation.TicketService
  - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
  - ubic.gemma.persistence.service.blacklist.BlacklistedEntityService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
  - ubic.gemma.persistence.service.expression.biomaterial.CompoundService
  - ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
  - ubic.gemma.persistence.service.association.Gene2GOAssociationService
  - ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService<C> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService<C>)
    - ubic.gemma.persistence.service.common.protocol.ProtocolService
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C> (also extends ubic.gemma.persistence.service.BaseService<O>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
- ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>
  - ubic.gemma.persistence.service.common.description.BibliographicReferenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
  - ubic.gemma.persistence.service.genome.biosequence.BioSequenceService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>)
  - ubic.gemma.persistence.service.blacklist.BlacklistedEntityService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>)
  - ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.FilteringService<O>)
    - ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
    - ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>)
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService<O>)
  - ubic.gemma.persistence.service.expression.experiment.GeeqService
  - ubic.gemma.persistence.service.genome.gene.GeneProductService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService<C>)
    - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
- ubic.gemma.persistence.service.expression.bioAssayData.BulkExpressionDataVectorService<T>
  - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
  - ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService
  - ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
- ubic.gemma.persistence.service.genome.ChromosomeService
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
- ubic.gemma.persistence.service.FilteringService<O>
  - ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    - ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
    - ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseService<O>)
    - ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.AdminEditableBaseImmutableService<O>)
- ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService<C>
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService<C> (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    - ubic.gemma.persistence.service.common.protocol.ProtocolService
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C> (also extends ubic.gemma.persistence.service.BaseService<O>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
      - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
      - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService (also extends ubic.gemma.persistence.service.analysis.AnalysisService<T>)
      - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      - ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
      - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
ubic.gemma.core.security.authentication.BaseUserService
- ubic.gemma.core.security.authentication.UserService
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService
ubic.gemma.persistence.service.common.description.BibliographicReferenceReadService
ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadService
ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadService
ubic.gemma.persistence.service.genome.biosequence.BioSequenceReadService
ubic.gemma.core.analysis.sequence.Blat
ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationReadService
ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultReadService
ubic.gemma.persistence.cache.CacheKeyLock
java.util.concurrent.Callable<V>
- ubic.gemma.core.loader.entrez.EntrezUtils.EntrezCall<T>
- ubic.gemma.core.job.Task<C>
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTask
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTask
  - ubic.gemma.core.tasks.maintenance.ArrayDesignReportTask
  - ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTask
  - ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTask
  - ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTask
  - ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTask
  - ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTask
  - ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTask
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTask
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTask
  - ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTask
  - ubic.gemma.core.tasks.analysis.expression.GeeqTask
  - ubic.gemma.core.tasks.maintenance.GeoScrapeTask
  - ubic.gemma.core.tasks.maintenance.IndexerTask
  - ubic.gemma.core.tasks.maintenance.MultifunctionalityTask
  - ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTask
  - ubic.gemma.core.tasks.analysis.expression.PreprocessExperimentTask
  - ubic.gemma.core.tasks.analysis.expression.SvdTask
ubic.gemma.core.visualization.cellbrowser.CellBrowserService
ubic.gemma.core.loader.expression.cellxgene.CellXGeneDataLoaderService
ubic.gemma.persistence.service.common.description.CharacteristicReadService
ubic.gemma.core.ontology.chembl.ChemblCodeResolver
ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadService
ubic.gemma.core.loader.util.converter.Converter<S,T>
- ubic.gemma.core.loader.expression.geo.GeoConverter
ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>
- ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDao
ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDecisionService
ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationDetailsService
ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService
ubic.gemma.persistence.service.common.description.DatabaseEntryReadService
ubic.gemma.core.loader.expression.DataLoaderConfigurer<T,C>
- ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfigurer<T>
ubic.gemma.core.loader.expression.DataUpdater
ubic.gemma.core.loader.expression.DataUpdaterAuditService
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisReadService
ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileService
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerAuditService
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultReadService
ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
ubic.gemma.persistence.service.expression.experiment.EeWriteService
ubic.gemma.core.loader.util.mapper.EntityMapper<T>
- ubic.gemma.core.loader.util.mapper.BioAssayMapper
- ubic.gemma.core.loader.util.mapper.DesignElementMapper
- ubic.gemma.core.loader.util.mapper.HintingEntityMapper<T>
ubic.gemma.core.loader.util.mapper.EntityMapper.StatefulEntityMapper<T>
java.util.concurrent.Executor
- ubic.gemma.core.util.concurrent.DelegatingExecutor
  - ubic.gemma.core.util.concurrent.DelegatingExecutorService (also extends java.util.concurrent.ExecutorService)
    - ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService (also extends java.util.concurrent.ScheduledExecutorService)
- java.util.concurrent.ExecutorService (also extends java.lang.AutoCloseable)
  - ubic.gemma.core.util.concurrent.DelegatingExecutorService (also extends ubic.gemma.core.util.concurrent.DelegatingExecutor)
    - ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService (also extends java.util.concurrent.ScheduledExecutorService)
  - java.util.concurrent.ScheduledExecutorService
    - ubic.gemma.core.util.concurrent.DelegatingScheduledExecutorService (also extends ubic.gemma.core.util.concurrent.DelegatingExecutorService)
- org.springframework.core.task.TaskExecutor
  - org.springframework.core.task.AsyncTaskExecutor
    - ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor (also extends ubic.gemma.core.util.concurrent.DelegatingTaskExecutor)
      - ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor (also extends org.springframework.scheduling.SchedulingTaskExecutor)
    - org.springframework.scheduling.SchedulingTaskExecutor
      - ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor (also extends ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor)
  - ubic.gemma.core.util.concurrent.DelegatingTaskExecutor
    - ubic.gemma.core.util.concurrent.DelegatingAsyncTaskExecutor (also extends org.springframework.core.task.AsyncTaskExecutor)
      - ubic.gemma.core.util.concurrent.DelegatingSchedulingTaskExecutor (also extends org.springframework.scheduling.SchedulingTaskExecutor)
ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter
ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignReadService
ubic.gemma.core.visualization.ExperimentalDesignVisualizationService
ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorReadService
ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService
ubic.gemma.core.analysis.service.ExpressionDataDeleterService
ubic.gemma.core.analysis.service.ExpressionDataFileService
ubic.gemma.core.analysis.preprocess.filter.ExpressionDataFilter<T>
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>
- ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix<T>
  - ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix (also extends ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix)
  - ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveIntMatrix (also extends ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix)
  - ubic.gemma.core.datastructure.matrix.MultiAssayBulkExpressionDataMatrix<T>
  - ubic.gemma.core.datastructure.matrix.SingleCellDerivedBulkExpressionDataMatrix<T>
- ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveDoubleMatrix
  - ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveDoubleMatrix (also extends ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix<T>)
- ubic.gemma.core.datastructure.matrix.ExpressionDataPrimitiveIntMatrix
  - ubic.gemma.core.datastructure.matrix.BulkExpressionDataPrimitiveIntMatrix (also extends ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix<T>)
- ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataMatrix<T>
ubic.gemma.core.analysis.service.ExpressionDataMatrixService
ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter<T,VT>
- ubic.gemma.core.datastructure.matrix.io.BulkExpressionDataMatrixWriter
- ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter
ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentGeoService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadService
ubic.gemma.core.analysis.report.ExpressionExperimentReportService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetReadService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteAuditService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteService
ubic.gemma.core.analysis.service.ExpressionMetadataChangelogFileService
ubic.gemma.persistence.service.common.description.ExternalDatabaseReadService
ubic.gemma.persistence.service.common.description.ExternalDatabaseReleaseAuditService
ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion
ubic.gemma.persistence.service.expression.experiment.FactorValueNeedsAttentionService
ubic.gemma.core.ontology.FactorValueOntologyService
ubic.gemma.core.ontology.FactorValueOntologyUtils.StatementVisitor<U,E>
ubic.gemma.persistence.service.expression.experiment.FactorValueReadService
org.springframework.beans.factory.FactoryBean<T>
- ubic.gemma.core.context.AsyncFactoryBean<T>
ubic.gemma.core.loader.genome.FastaCmd
ubic.gemma.core.loader.util.fetcher.Fetcher
- ubic.gemma.core.loader.util.fetcher.ArchiveFetcher
ubic.gemma.core.util.locking.FileLockManager
ubic.gemma.core.util.matrix.datafilter.Filter<M,R,C,V>
ubic.gemma.core.loader.util.ftp.FTPClientAuthenticator
ubic.gemma.core.loader.util.ftp.FTPClientFactory
ubic.gemma.persistence.service.expression.experiment.GeeqAuditService
ubic.gemma.core.util.GemmaRestApiClient
ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
ubic.gemma.core.util.GemmaRestApiClient.Response
- ubic.gemma.core.util.GemmaRestApiClient.DataResponse
- ubic.gemma.core.util.GemmaRestApiClient.EmptyResponse
- ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse
ubic.gemma.model.common.GemmaSessionBackedValueObject
ubic.gemma.persistence.service.association.Gene2GOAssociationReadService
ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService
ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService
ubic.gemma.persistence.service.genome.gene.GeneProductReadService
ubic.gemma.persistence.service.genome.gene.GeneReadService
ubic.gemma.persistence.service.genome.gene.GeneSearchService
ubic.gemma.persistence.service.genome.gene.GeneSetReadService
ubic.gemma.core.search.GeneSetSearch
ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
ubic.gemma.persistence.service.genome.gene.GeneWriteService
ubic.gemma.core.loader.expression.geo.service.GeoBrowser
ubic.gemma.core.geoscrape.GeoRecordMatcher
ubic.gemma.core.geoscrape.GeoScrapeService
ubic.gemma.core.loader.expression.geo.service.GeoService
ubic.gemma.core.loader.expression.geo.service.GeoUpdateAuditService
ubic.gemma.core.search.getOntologyTermFormatter
ubic.gemma.core.goldenpath.GoldenPathQueryFactory
ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysisFactory
ubic.gemma.core.ontology.GoMetric
org.springframework.security.provisioning.GroupManager
- ubic.gemma.core.security.authentication.GroupManager
  - ubic.gemma.core.security.authentication.UserManager (also extends ubic.gemma.core.security.authentication.UserDetailsManager)
ubic.gemma.core.search.Highlighter
- ubic.gemma.core.search.OntologyHighlighter
ubic.gemma.core.analysis.report.HomeStatsService
ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
ubic.gemma.model.common.Identifiable
- ubic.gemma.model.common.Describable
  - ubic.gemma.model.expression.experiment.BioAssaySetValueObject (also extends ubic.gemma.core.security.model.SecureValueObject, java.io.Serializable)
  - ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics
- ubic.gemma.model.common.auditAndSecurity.Securable (also extends ubic.gemma.core.security.model.Securable)
  - ubic.gemma.model.common.auditAndSecurity.Auditable
    - ubic.gemma.model.common.auditAndSecurity.curation.Curatable
  - ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT> (also extends ubic.gemma.core.security.model.SecuredChild)
  - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends ubic.gemma.core.security.model.SecuredNotChild)
ubic.gemma.core.search.indexer.IndexerService
org.springframework.beans.factory.InitializingBean
- ubic.gemma.core.logging.log4j.ThreadContextPopulator
java.lang.Iterable<T>
- java.util.Collection<E>
  - java.util.SequencedCollection<E>
    - java.util.List<E>
      - ubic.gemma.core.datastructure.sparse.SparseList<T>
- ubic.gemma.core.loader.util.anndata.Dataframe.Column<K,T>
ubic.gemma.core.mail.MailEngine
ubic.gemma.core.mail.MailService
ubic.gemma.core.security.authentication.ManualAuthenticationService
ubic.gemma.core.util.matrix.Matrix2D<R,C,V>
- ubic.gemma.core.util.matrix.ObjectMatrix<R,C,V>
- ubic.gemma.core.util.matrix.PrimitiveMatrix<R,C,V>
ubic.gemma.core.analysis.preprocess.MeanVarianceService
ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
io.micrometer.core.instrument.binder.MeterBinder
- ubic.gemma.core.job.TaskRunningService
ubic.gemma.core.security.acl.ObjectTransientnessRetrievalStrategy
ubic.gemma.core.ontology.ObsoleteTermCorrectionService
ubic.gemma.core.ontology.ols.OlsTermResolver
ubic.gemma.core.ontology.model.OntologyModel
ubic.gemma.core.ontology.relation.OntologyRelationProducer
ubic.gemma.core.ontology.model.OntologyResource
- ubic.gemma.core.ontology.model.AnnotationProperty
- ubic.gemma.core.ontology.model.OntologyIndividual
- ubic.gemma.core.ontology.model.OntologyProperty
  - ubic.gemma.core.ontology.model.DatatypeProperty
  - ubic.gemma.core.ontology.model.ObjectProperty
- ubic.gemma.core.ontology.model.OntologyTerm
  - ubic.gemma.core.ontology.model.OntologyRestriction
    - ubic.gemma.core.ontology.model.OntologyCardinalityRestriction
    - ubic.gemma.core.ontology.model.OntologyClassRestriction
    - ubic.gemma.core.ontology.model.OntologyDatatypeRestriction
ubic.gemma.core.ontology.search.OntologySearchService
ubic.gemma.core.ontology.OntologyService
ubic.gemma.core.ontology.model.OntologyStatement
ubic.gemma.core.ontology.OntologyTermValidator
ubic.gemma.core.analysis.preprocess.OutlierDetectionService
ubic.gemma.core.analysis.service.OutlierFlaggingAuditService
ubic.gemma.core.analysis.service.OutlierFlaggingService
ubic.gemma.core.security.authorization.acl.ParentIdentityRetrievalStrategy
ubic.gemma.core.loader.util.parser.Parser<T>
- ubic.gemma.core.loader.util.parser.LineParser<T>
ubic.gemma.persistence.persister.Persister
- ubic.gemma.persistence.persister.PersisterHelper
ubic.gemma.persistence.service.pipeline.PipelineJobBatchService
ubic.gemma.core.pipeline.PipelineScheduler
ubic.gemma.persistence.service.expression.experiment.PreboardedAuditService
ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService
ubic.gemma.core.analysis.preprocess.PreprocessorHelperService
ubic.gemma.core.analysis.preprocess.PreprocessorService
ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisReadService
ubic.gemma.core.analysis.sequence.ProbeMapper
ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorAuditService
ubic.gemma.core.util.ProgressReporterFactory
ubic.gemma.core.job.progress.ProgressUpdateCallback
ubic.gemma.persistence.util.PropertyMapping
ubic.gemma.persistence.service.common.protocol.ProtocolReadService
ubic.gemma.persistence.service.common.description.PublicationAssociationService
ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeReadService
ubic.gemma.core.loader.util.QueuingParser<T>
org.hibernate.query.ResultListTransformer<T>
- ubic.gemma.persistence.hibernate.TypedResultTransformer<T> (also extends org.hibernate.query.TupleTransformer<T>)
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAuditService
ubic.gemma.core.analysis.preprocess.batcheffects.ScanDateExtractor
ubic.gemma.core.search.SearchService
ubic.gemma.core.search.SearchService.SearchResultMap
ubic.gemma.core.search.SearchSource
- ubic.gemma.core.search.FieldAwareSearchSource
ubic.gemma.core.security.model.Securable
- ubic.gemma.model.common.auditAndSecurity.Securable (also extends ubic.gemma.model.common.Identifiable)
  - ubic.gemma.model.common.auditAndSecurity.Auditable
    - ubic.gemma.model.common.auditAndSecurity.curation.Curatable
  - ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT> (also extends ubic.gemma.core.security.model.SecuredChild)
  - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends ubic.gemma.core.security.model.SecuredNotChild)
- ubic.gemma.core.security.model.SecuredChild
  - ubic.gemma.model.common.auditAndSecurity.SecuredChild<OT> (also extends ubic.gemma.model.common.auditAndSecurity.Securable)
- ubic.gemma.core.security.model.SecuredNotChild
  - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends ubic.gemma.model.common.auditAndSecurity.Securable)
  - ubic.gemma.core.security.model.User (also extends ubic.gemma.core.security.model.Securable)
  - ubic.gemma.core.security.model.UserGroup
- ubic.gemma.core.security.model.SecureValueObject
  - ubic.gemma.model.expression.experiment.BioAssaySetValueObject (also extends ubic.gemma.model.common.Describable, java.io.Serializable)
- ubic.gemma.core.security.model.User (also extends ubic.gemma.core.security.model.SecuredNotChild)
ubic.gemma.core.security.SecurityService
ubic.gemma.core.analysis.preprocess.qc.SequencingQcMetricsService
java.io.Serializable
- ubic.gemma.core.util.math.linearmodels.AnovaResult
  - ubic.gemma.core.util.math.linearmodels.GenericAnovaResult
  - ubic.gemma.core.util.math.linearmodels.OneWayAnovaResult
  - ubic.gemma.core.util.math.linearmodels.TwoWayAnovaResult
- ubic.gemma.model.expression.experiment.BioAssaySetValueObject (also extends ubic.gemma.model.common.Describable, ubic.gemma.core.security.model.SecureValueObject)
- org.springframework.security.core.GrantedAuthority
  - ubic.gemma.core.security.model.GroupAuthority
- ubic.gemma.core.visualization.Heatmap
- ubic.gemma.core.util.math.linearmodels.LinearModelSummary
ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
ubic.gemma.core.util.SimpleRetryCallable<T,E>
ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderService
ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformation
- ubic.gemma.core.loader.expression.singleCell.transform.CellRangerBasedTransformation
- ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation
- ubic.gemma.core.loader.expression.singleCell.transform.SingleCellInputOutputFileTransformation
ubic.gemma.core.loader.expression.singleCell.transform.SingleCellDataTransformationFactory
ubic.gemma.core.loader.expression.geo.singleCell.SingleCellDetector
- ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector
- ubic.gemma.core.loader.expression.geo.singleCell.SeriesAwareSingleCellDetector
ubic.gemma.persistence.service.expression.experiment.SingleCellExperimentDesignAuditService
ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateAuditService
ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateService
ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentCreateSubSetsAndAggregateService
ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService
ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetAuditService
ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentSubSetService
ubic.gemma.core.loader.util.sdo.SourceDomainObjectGenerator
ubic.gemma.core.analysis.preprocess.SplitExperimentService
ubic.gemma.core.job.SubmittedTask
ubic.gemma.core.analysis.preprocess.svd.SVDService
ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
ubic.gemma.core.job.notification.TaskMailUtils
ubic.gemma.core.job.notification.TaskPostProcessing
ubic.gemma.persistence.service.genome.taxon.TaxonReadService
org.hibernate.query.TupleTransformer<T>
- ubic.gemma.persistence.hibernate.TypedResultTransformer<T> (also extends org.hibernate.query.ResultListTransformer<T>)
ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService
ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
org.springframework.security.core.userdetails.UserDetailsService
- org.springframework.security.provisioning.UserDetailsManager
  - ubic.gemma.core.security.authentication.UserDetailsManager
    - ubic.gemma.core.security.authentication.UserManager (also extends ubic.gemma.core.security.authentication.GroupManager)
ubic.gemma.core.security.authentication.UserReadService
ubic.gemma.core.analysis.preprocess.VectorMergingService
ubic.gemma.model.common.description.Versioned
ubic.gemma.core.analysis.report.WhatsNewService
ubic.gemma.persistence.service.expression.experiment.WorkflowService

Annotation Interface Hierarchy

ubic.gemma.core.security.audit.Audited (implements java.lang.annotation.Annotation)
ubic.gemma.core.security.audit.AuditedConditional (implements java.lang.annotation.Annotation)
ubic.gemma.core.security.audit.AuditedOnError (implements java.lang.annotation.Annotation)
ubic.gemma.core.security.audit.AuditedOnErrors (implements java.lang.annotation.Annotation)
ubic.gemma.model.annotations.GemmaRestOnly (implements java.lang.annotation.Annotation)
ubic.gemma.core.security.acl.annotation.IgnoreAcl (implements java.lang.annotation.Annotation)
ubic.gemma.model.annotations.MayBeUninitialized (implements java.lang.annotation.Annotation)
ubic.gemma.persistence.retry.Retryable (implements java.lang.annotation.Annotation)
ubic.gemma.core.architecture.SuppressArchUnit (implements java.lang.annotation.Annotation)
ubic.gemma.core.context.TestComponent (implements java.lang.annotation.Annotation)
ubic.gemma.model.common.ValueObject (implements java.lang.annotation.Annotation)
ubic.gemma.model.annotations.WithheldFromApi (implements java.lang.annotation.Annotation)

Enum Class Hierarchy

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
  - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
  - ubic.gemma.model.expression.experiment.AgentCurationKind
  - ubic.gemma.core.analysis.expression.diff.AnalysisType
  - ubic.gemma.model.common.description.AnnotationRelationBasis
  - ubic.gemma.persistence.service.common.description.AnnotationRelationDao.Direction
  - ubic.gemma.model.common.description.AnnotationRelationStatus
  - ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetDao.SummarySort
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetRole
  - ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSource
  - ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
  - ubic.gemma.model.common.auditAndSecurity.AuditAction
  - ubic.gemma.model.expression.experiment.BatchEffectType
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionScope
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDecisionType
  - ubic.gemma.model.common.auditAndSecurity.curation.CurationDraftDispositions.Disposition
  - ubic.gemma.persistence.util.Cursor.Direction
  - ubic.gemma.model.common.description.DatabaseType
  - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter.RepetitiveValuesFilterMode
  - ubic.gemma.model.analysis.expression.diff.Direction
  - ubic.gemma.core.loader.entrez.EntrezRetmode
  - ubic.gemma.core.analysis.service.ExpressionExperimentDataFileType
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
  - ubic.gemma.model.common.auditAndSecurity.curation.ExternalIssueSyncState
  - ubic.gemma.model.expression.bioAssay.ExtractedMolecule
  - ubic.gemma.model.expression.experiment.FactorType
  - ubic.gemma.core.loader.expression.cellxgene.FileType
  - ubic.gemma.persistence.util.Filter.Operator
  - ubic.gemma.model.common.auditAndSecurity.curation.FindingDisposition
  - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
  - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
  - ubic.gemma.model.common.quantitationtype.GeneralType
  - ubic.gemma.core.loader.expression.geo.service.GeoAmount
  - ubic.gemma.core.loader.expression.geo.model.GeoChannel.ChannelMolecule
  - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ExperimentType
  - ubic.gemma.core.loader.expression.geo.model.GeoDataset.PlatformType
  - ubic.gemma.core.loader.expression.geo.model.GeoDataset.SampleType
  - ubic.gemma.core.loader.expression.geo.model.GeoDataset.ValueType
  - ubic.gemma.core.loader.expression.geo.service.GeoFormat
  - ubic.gemma.core.loader.expression.geo.GeoLibrarySource
  - ubic.gemma.core.loader.expression.geo.model.GeoLibraryStrategy
  - ubic.gemma.core.loader.expression.geo.service.GeoRecordType
  - ubic.gemma.core.loader.expression.geo.model.GeoReplication.ReplicationType
  - ubic.gemma.core.loader.expression.geo.GeoSampleType
  - ubic.gemma.core.loader.expression.geo.service.GeoScope
  - ubic.gemma.model.expression.experiment.GeoScrapeWatermark.Status
  - ubic.gemma.core.loader.expression.geo.service.GeoSearchField
  - ubic.gemma.core.loader.expression.geo.model.GeoSeriesType
  - ubic.gemma.core.loader.expression.geo.service.GeoSource
  - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
  - ubic.gemma.model.association.GOEvidenceCode
  - ubic.gemma.core.ontology.GoMetric.Metric
  - ubic.gemma.core.loader.util.hdf5.H5FundamentalType
  - ubic.gemma.model.pipeline.JobState
  - ubic.gemma.model.common.measurement.MeasurementKind
  - ubic.gemma.model.common.measurement.MeasurementType
  - ubic.gemma.core.loader.expression.ucsc.cellbrowser.model.MetaFieldType
  - ubic.gemma.model.util.ModelUtils.EqualityOutcome
  - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
  - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
  - ubic.gemma.core.ontology.model.OntologyCardinalityRestriction.CardinalityType
  - ubic.gemma.core.ontology.providers.OntologyService.InferenceMode
  - ubic.gemma.core.ontology.providers.OntologyService.LanguageLevel
  - ubic.gemma.core.ontology.model.OntologyXref.Strength
  - ubic.gemma.model.pipeline.PipelineJobBatch.BatchState
  - ubic.gemma.model.genome.biosequence.PolymerType
  - ubic.gemma.model.common.quantitationtype.PrimitiveType
  - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
  - ubic.gemma.model.common.description.PublicationAssociationRole
  - ubic.gemma.model.common.description.PublicationAssociationSource
  - ubic.gemma.model.common.description.PublicationAssociationStatus
  - ubic.gemma.model.common.description.RelationInferenceDirection
  - ubic.gemma.model.common.description.RelationTopicality
  - ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter.Mode
  - ubic.gemma.model.common.quantitationtype.ScaleType
  - ubic.gemma.model.pipeline.SchedulerKind
  - ubic.gemma.model.common.auditAndSecurity.curation.ScreeningResult
  - ubic.gemma.model.common.search.SearchMatchType
  - ubic.gemma.model.common.search.SearchSettings.SearchMode
  - ubic.gemma.model.genome.biosequence.SequenceType
  - ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome
  - ubic.gemma.core.loader.expression.singleCell.SingleCellDataType
  - ubic.gemma.core.analysis.singleCell.aggregate.SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod
  - ubic.gemma.core.analysis.singleCell.aggregate.SingleCellExpressionExperimentAggregateServiceImpl.SingleCellExpressionAggregationMethod
  - ubic.gemma.persistence.service.expression.experiment.SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome
  - ubic.gemma.core.visualization.SingleCellSparsityHeatmap.SingleCellHeatmapType
  - ubic.gemma.persistence.util.Sort.Direction
  - ubic.gemma.persistence.util.Sort.NullMode
  - ubic.gemma.model.common.quantitationtype.StandardQuantitationType
  - ubic.gemma.core.job.SubmittedTask.Status
  - ubic.gemma.persistence.util.SubqueryMode
  - ubic.gemma.model.expression.arrayDesign.TechnologyType
  - ubic.gemma.core.ontology.TermViolation.Reason
  - ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketEventType
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketMode
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketPriority
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketState
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetStatus
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetType
  - ubic.gemma.model.common.auditAndSecurity.curation.TicketType
  - ubic.gemma.model.common.auditAndSecurity.curation.TriageJudgeKind
  - ubic.gemma.model.common.auditAndSecurity.curation.TriageVerdict
  - ubic.gemma.model.annotations.WithheldFromApi.Reason
  - ubic.gemma.model.expression.experiment.WorkflowState

Record Class Hierarchy

java.lang.Object
- java.lang.Record
  - ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject.LastEventTriple
  - ubic.gemma.core.security.audit.AuditEventPayload.None (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao.BioSequenceLite
  - ubic.gemma.core.util.runtime.CpuInfo
  - ubic.gemma.core.security.audit.payload.DifferentialExpressionAnalysisPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.model.expression.experiment.ExpressionExperimentIdAndShortName (implements ubic.gemma.model.common.Identifiable)
  - ubic.gemma.core.ontology.lexical.LexicalOntologyIndex.Hit
  - ubic.gemma.core.ontology.lexical.LexicalTerm
  - ubic.gemma.core.ontology.lexical.LexicalTermMetadata
  - ubic.gemma.core.ontology.lexical.LexicalTermMetadata.Taxon
  - ubic.gemma.core.util.runtime.MemInfo
  - ubic.gemma.core.security.audit.payload.ProcessedVectorComputationPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.core.security.audit.payload.ReleaseDetailsUpdatePayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterConfig
  - ubic.gemma.core.security.audit.payload.SampleCorrelationAnalysisPayload.FilterStage
  - ubic.gemma.core.security.audit.payload.SampleRemovalPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)
  - ubic.gemma.core.security.audit.payload.SingleCellAggregationPayload.AggregatedAssay
  - ubic.gemma.core.security.audit.payload.SingleCellSubSetsCreatedPayload (implements ubic.gemma.core.security.audit.AuditEventPayload)

Hierarchy For All Packages

Class Hierarchy

Interface Hierarchy

Annotation Interface Hierarchy

Enum Class Hierarchy

Record Class Hierarchy