Class Hierarchy (Gemma 1.31.11-SNAPSHOT API)

Class Hierarchy

java.lang.Object
- ubic.gemma.core.image.aba.AbaGene
- ubic.gemma.core.image.ABALinkOutValueObject (implements java.io.Serializable)
- org.springframework.security.acls.afterinvocation.AbstractAclProvider (implements org.springframework.security.access.AfterInvocationProvider)
  - org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
    - gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
      - gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
        
        ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
        
        ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
  - org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationProvider (implements org.springframework.context.MessageSourceAware)
    - gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider
      - ubic.gemma.core.security.authorization.acl.AclAfterCompSeqByArrayDesignFilter
- ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
  - ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer (implements ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer)
    - ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer (implements org.springframework.beans.factory.DisposableBean)
- ubic.gemma.rest.util.args.AbstractArg<T> (implements ubic.gemma.rest.util.args.Arg<T>)
  - ubic.gemma.rest.util.args.AbstractArrayArg<T>
    - ubic.gemma.rest.util.args.AbstractEntityArrayArg<O,S> (implements ubic.gemma.rest.util.args.Arg<T>)
      - ubic.gemma.rest.util.args.CompositeSequenceArrayArg
      - ubic.gemma.rest.util.args.DatabaseEntryArrayArg
      - ubic.gemma.rest.util.args.DatasetArrayArg
      - ubic.gemma.rest.util.args.GeneArrayArg
      - ubic.gemma.rest.util.args.PlatformArrayArg
      - ubic.gemma.rest.util.args.TaxonArrayArg
    - ubic.gemma.rest.util.args.ExcludeArg<T>
    - ubic.gemma.rest.util.args.StringArrayArg
  - ubic.gemma.rest.util.args.AbstractEntityArg<T,O,S> (implements ubic.gemma.rest.util.args.Arg<T>)
    - ubic.gemma.rest.util.args.CompositeSequenceArg<T>
      - ubic.gemma.rest.util.args.CompositeSequenceIdArg
      - ubic.gemma.rest.util.args.CompositeSequenceNameArg
    - ubic.gemma.rest.util.args.DatabaseEntryArg<T>
      - ubic.gemma.rest.util.args.DatabaseEntryIdArg
      - ubic.gemma.rest.util.args.DatabaseEntryStringArg
    - ubic.gemma.rest.util.args.DatasetArg<T>
      - ubic.gemma.rest.util.args.DatasetIdArg
      - ubic.gemma.rest.util.args.DatasetStringArg
    - ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
    - ubic.gemma.rest.util.args.FactorValueArg<A>
      - ubic.gemma.rest.util.args.FactorValueIdArg
      - ubic.gemma.rest.util.args.FactorValueValueArg
    - ubic.gemma.rest.util.args.GeneArg<T>
      - ubic.gemma.rest.util.args.GeneEnsemblIdArg
      - ubic.gemma.rest.util.args.GeneNcbiIdArg
      - ubic.gemma.rest.util.args.GeneSymbolArg
    - ubic.gemma.rest.util.args.PlatformArg<T>
      - ubic.gemma.rest.util.args.PlatformIdArg
      - ubic.gemma.rest.util.args.PlatformStringArg
    - ubic.gemma.rest.util.args.QuantitationTypeArg<T>
      - ubic.gemma.rest.util.args.QuantitationTypeByIdArg
      - ubic.gemma.rest.util.args.QuantitationTypeByNameArg
    - ubic.gemma.rest.util.args.TaxonArg<T>
      - ubic.gemma.rest.util.args.TaxonIdArg
      - ubic.gemma.rest.util.args.TaxonNameArg
      - ubic.gemma.rest.util.args.TaxonNcbiIdArg
  - ubic.gemma.rest.util.args.ExpLevelConsolidationArg
  - ubic.gemma.rest.util.args.FilterArg<O>
  - ubic.gemma.rest.util.args.LimitArg
  - ubic.gemma.rest.util.args.OffsetArg
  - ubic.gemma.rest.util.args.SortArg<O>
- ubic.gemma.core.context.AbstractAsyncFactoryBean<T> (implements ubic.gemma.core.context.AsyncFactoryBean<T>, org.springframework.beans.factory.DisposableBean)
  - ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
- ubic.gemma.core.util.AbstractCLI (implements ubic.gemma.core.util.CLI)
  - ubic.gemma.core.util.AbstractAuthenticatedCLI
    - ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
    - ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
      - ubic.gemma.core.apps.AffyProbeCollapseCli
      - ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
      - ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
      - ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
      - ubic.gemma.core.apps.ArrayDesignBlatCli
      - ubic.gemma.core.apps.ArrayDesignMapSummaryCli
      - ubic.gemma.core.apps.ArrayDesignMergeCli
      - ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
      - ubic.gemma.core.apps.ArrayDesignProbeMapperCli
      - ubic.gemma.core.apps.ArrayDesignProbeRenamerCli
      - ubic.gemma.core.apps.ArrayDesignRepeatScanCli
      - ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
      - ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
      - ubic.gemma.core.apps.BioSequenceCleanupCli
    - ubic.gemma.core.apps.BibRefUpdaterCli
    - ubic.gemma.core.apps.BlacklistCli
    - ubic.gemma.core.apps.DatabaseViewGeneratorCLI
    - ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
    - ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI
      - ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
    - ubic.gemma.core.apps.ExperimentalDesignImportCli
    - ubic.gemma.core.apps.ExperimentalDesignViewCli
    - ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
      - ubic.gemma.core.apps.AffyDataFromCelCli
      - ubic.gemma.core.apps.BatchEffectPopulationCli
      - ubic.gemma.core.apps.DeleteDiffExCli
      - ubic.gemma.core.apps.DeleteExperimentsCli
      - ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
      - ubic.gemma.core.apps.ExperimentalDesignWriterCLI
      - ubic.gemma.core.apps.ExpressionDataCorrMatCli
      - ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
      - ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
      - ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
      - ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
      - ubic.gemma.core.apps.GeeqCli
      - ubic.gemma.core.apps.LinkAnalysisCli
      - ubic.gemma.core.apps.MakeExperimentPrivateCli
      - ubic.gemma.core.apps.MakeExperimentsPublicCli
      - ubic.gemma.core.apps.OrderVectorsByDesignCli
      - ubic.gemma.core.apps.ProcessedDataComputeCLI
      - ubic.gemma.core.apps.RefreshExperimentCli
      - ubic.gemma.core.apps.ReplaceDataCli
      - ubic.gemma.core.apps.RNASeqBatchInfoCli
      - ubic.gemma.core.apps.RNASeqDataAddCli
      - ubic.gemma.core.apps.SplitExperimentCli
      - ubic.gemma.core.apps.SVDCli
      - ubic.gemma.core.apps.VectorMergingCli
    - ubic.gemma.core.apps.ExternalDatabaseAdderCli
    - ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI
      - ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
      - ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
      - ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli
      - ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli
      - ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli
      - ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli
    - ubic.gemma.core.apps.ExternalDatabaseOverviewCli
    - ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
    - ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
    - ubic.gemma.core.apps.FactorValueMigratorCLI
    - ubic.gemma.core.apps.FindObsoleteTermsCli
    - ubic.gemma.core.apps.FixOntologyTermLabelsCli
    - ubic.gemma.core.apps.GenericGenelistDesignGenerator
    - ubic.gemma.core.apps.GeoGrabberCli
    - ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
    - ubic.gemma.core.apps.LoadExpressionDataCli
    - ubic.gemma.core.apps.LoadSimpleExpressionDataCli
    - ubic.gemma.core.apps.MultifunctionalityCli
    - ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
    - ubic.gemma.core.apps.NcbiGeneLoaderCLI
    - ubic.gemma.core.apps.PubMedLoaderCli
    - ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
    - ubic.gemma.core.apps.TaxonLoaderCli
    - ubic.gemma.core.apps.UpdateEe2AdCli
    - ubic.gemma.core.apps.UpdateEE2CCli
    - ubic.gemma.core.apps.UpdateGene2CsCli
    - ubic.gemma.core.apps.UpdatePubMedCli
  - ubic.gemma.core.apps.GenerateDatabaseUpdateCli
  - ubic.gemma.core.apps.IndexGemmaCLI
  - ubic.gemma.core.apps.InitializeDatabaseCli
  - ubic.gemma.core.apps.MeshTermFetcherCli
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
  - java.util.AbstractList<E> (implements java.util.List<E>)
    - ubic.gemma.persistence.util.Slice<O> (implements java.util.List<E>)
  - java.util.AbstractSet<E> (implements java.util.Set<E>)
    - ubic.gemma.core.search.SearchResultSet<T>
- 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.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.association.coexpression.CoexpressionNodeDegreeDaoImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDao)
  - 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.association.phenotype.DifferentialExpressionEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDao)
  - 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.association.phenotype.ExperimentalEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDao)
  - 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.association.phenotype.GenericEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.GenericEvidenceDao)
  - ubic.gemma.persistence.service.association.phenotype.GenericExperimentDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.GenericExperimentDao)
  - 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.association.phenotype.LiteratureEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDao)
  - ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao)
  - ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao)
  - 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.association.ReferenceAssociationDaoImpl (implements ubic.gemma.persistence.service.association.ReferenceAssociationDao)
  - ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase<T> (implements ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao<T>)
    - ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao)
  - ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.StatementDao)
  - 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.model.common.AbstractDescribable (implements ubic.gemma.model.common.Describable)
  - ubic.gemma.model.common.auditAndSecurity.AbstractAuditable (implements ubic.gemma.model.common.auditAndSecurity.Auditable, java.io.Serializable)
    - 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)
      - ubic.gemma.model.association.phenotype.GenericExperiment
    - ubic.gemma.model.association.phenotype.PhenotypeAssociation (implements ubic.gemma.model.common.auditAndSecurity.Securable)
      - ubic.gemma.model.association.phenotype.DataAnalysisEvidence
        
        ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence
      - ubic.gemma.model.association.phenotype.ExperimentalEvidence
      - ubic.gemma.model.association.phenotype.GenericEvidence
      - ubic.gemma.model.association.phenotype.LiteratureEvidence
    - ubic.gemma.model.common.auditAndSecurity.UserGroup (implements gemma.gsec.model.UserGroup)
  - ubic.gemma.model.analysis.Analysis (implements java.io.Serializable)
    - 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 (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild)
        
        ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis
        
        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 (implements java.io.Serializable)
  - ubic.gemma.model.expression.bioAssay.BioAssay (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
  - ubic.gemma.model.expression.bioAssayData.BioAssayDimension (implements java.io.Serializable)
  - ubic.gemma.model.expression.biomaterial.BioMaterial (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
  - ubic.gemma.model.genome.biosequence.BioSequence (implements java.io.Serializable)
  - ubic.gemma.model.blacklist.BlacklistedEntity (implements java.io.Serializable)
    - ubic.gemma.model.blacklist.BlacklistedExperiment
    - ubic.gemma.model.blacklist.BlacklistedPlatform
  - ubic.gemma.model.common.description.Characteristic (implements java.lang.Comparable<T>, java.io.Serializable)
    - ubic.gemma.model.expression.experiment.Statement
  - ubic.gemma.model.genome.ChromosomeFeature (implements java.io.Serializable)
    - ubic.gemma.model.genome.Gene
    - ubic.gemma.model.genome.gene.GeneProduct
  - ubic.gemma.model.expression.designElement.CompositeSequence (implements java.io.Serializable)
  - ubic.gemma.model.expression.biomaterial.Compound (implements java.io.Serializable)
  - ubic.gemma.model.common.auditAndSecurity.Contact (implements java.io.Serializable)
    - ubic.gemma.model.common.auditAndSecurity.Person
      - ubic.gemma.model.common.auditAndSecurity.User (implements gemma.gsec.model.User)
  - ubic.gemma.model.expression.experiment.ExperimentalDesign (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
  - ubic.gemma.model.expression.experiment.ExperimentalFactor (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
  - ubic.gemma.model.common.description.ExternalDatabase (implements ubic.gemma.model.common.auditAndSecurity.Auditable, java.io.Serializable, ubic.gemma.model.common.description.Versioned)
  - ubic.gemma.model.common.protocol.Protocol (implements ubic.gemma.model.common.auditAndSecurity.Securable, java.io.Serializable)
  - ubic.gemma.model.common.quantitationtype.QuantitationType (implements java.io.Serializable)
  - ubic.gemma.core.loader.expression.arrayDesign.Reporter (implements java.io.Serializable)
  - ubic.gemma.model.expression.biomaterial.Treatment (implements java.io.Serializable)
- ubic.gemma.rest.util.args.AbstractEntityArgService<T,S> (implements ubic.gemma.rest.util.args.EntityArgService<T,S>)
  - ubic.gemma.rest.util.args.CompositeSequenceArgService
  - ubic.gemma.rest.util.args.DatabaseEntryArgService
  - ubic.gemma.rest.util.args.DatasetArgService
  - ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
  - ubic.gemma.rest.util.args.GeneArgService
  - ubic.gemma.rest.util.args.PlatformArgService
  - ubic.gemma.rest.util.args.QuantitationTypeArgService
  - ubic.gemma.rest.util.args.TaxonArgService
- ubic.gemma.rest.providers.AbstractExceptionMapper<E> (implements javax.ws.rs.ext.ExceptionMapper<E>)
  - ubic.gemma.rest.providers.AccessDeniedExceptionMapper
  - ubic.gemma.rest.providers.AuthenticationExceptionMapper
  - ubic.gemma.rest.providers.EntityNotFoundExceptionMapper
  - ubic.gemma.rest.providers.MalformedArgExceptionMapper
  - ubic.gemma.rest.providers.NotFoundExceptionMapper
  - ubic.gemma.rest.providers.UnhandledExceptionMapper
  - ubic.gemma.rest.providers.WebApplicationExceptionMapper
- 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.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.analysis.service.AbstractFileService<T> (implements ubic.gemma.core.analysis.service.JsonFileService<T>, ubic.gemma.core.analysis.service.TsvFileService<T>)
  - ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileServiceImpl (implements ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileService)
  - ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService)
  - ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionDataFileService)
  - ubic.gemma.core.datastructure.matrix.MatrixWriter
- ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
- ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
- ubic.gemma.core.loader.expression.geo.service.AbstractGeoService (implements org.springframework.beans.factory.BeanFactoryAware, ubic.gemma.core.loader.expression.geo.service.GeoService)
  - ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
- org.springframework.web.servlet.handler.AbstractHandlerExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver, org.springframework.core.Ordered)
  - ubic.gemma.web.util.ClientAbortExceptionResolver
- ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis (implements ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis)
  - ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
    - ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
- ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
  - ubic.gemma.core.metrics.MeterRegistryCliConfigurer (implements org.springframework.context.ApplicationContextAware)
  - ubic.gemma.core.metrics.MeterRegistryEhcacheConfigurer
  - ubic.gemma.web.metrics.MeterRegistryWebConfigurer
- io.swagger.v3.core.jackson.AbstractModelConverter (implements io.swagger.v3.core.converter.ModelConverter)
  - io.swagger.v3.core.jackson.ModelResolver (implements io.swagger.v3.core.converter.ModelConverter)
    - ubic.gemma.rest.swagger.resolver.CustomModelResolver
- ubic.gemma.core.ontology.AbstractOntologyResourceSimple (implements ubic.basecode.ontology.model.OntologyResource, java.io.Serializable)
  - ubic.gemma.core.ontology.OntologyIndividualSimple (implements ubic.basecode.ontology.model.OntologyIndividual)
  - ubic.gemma.core.ontology.OntologyPropertySimple (implements ubic.basecode.ontology.model.OntologyProperty)
- ubic.basecode.ontology.jena.AbstractOntologyService (implements ubic.basecode.ontology.providers.OntologyService)
  - ubic.basecode.ontology.providers.AbstractOntologyService
    - 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.MondoOntologyService
    - ubic.gemma.core.ontology.providers.PatoOntologyService
- ubic.gemma.persistence.persister.AbstractPersister (implements ubic.gemma.persistence.persister.Persister)
  - ubic.gemma.persistence.persister.CommonPersister
    - ubic.gemma.persistence.persister.GenomePersister
      - ubic.gemma.persistence.persister.ArrayDesignPersister
        
        ubic.gemma.persistence.persister.ExpressionPersister (implements ubic.gemma.persistence.persister.PersisterHelper)
        
        ubic.gemma.persistence.persister.RelationshipPersister
        
        ubic.gemma.persistence.persister.PersisterHelperImpl (implements ubic.gemma.persistence.persister.PersisterHelper)
- ubic.gemma.persistence.persister.AbstractPersister.Caches
- ubic.gemma.persistence.service.AbstractService<O> (implements ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService<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)
    - 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.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService)
  - ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundService)
  - ubic.gemma.persistence.service.common.auditAndSecurity.ContactServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.ContactService)
  - 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, org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService)
  - ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl (implements ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService)
  - 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.web.persistence.AbstractSetListContainer (implements java.io.Serializable)
  - ubic.gemma.web.persistence.ExperimentSetListContainer
  - ubic.gemma.web.persistence.GeneSetListContainer
- ubic.gemma.core.job.AbstractTask<C> (implements ubic.gemma.core.job.Task<C>)
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
  - ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskImpl (implements ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTask)
  - 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.maintenance.ExpressionExperimentReportTaskImpl (implements ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTask)
  - ubic.gemma.core.tasks.maintenance.IndexerTaskImpl (implements ubic.gemma.core.tasks.maintenance.IndexerTask)
  - ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskImpl
  - 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
- ubic.gemma.persistence.util.AclCriteriaUtils
- ubic.gemma.persistence.util.AclQueryUtils
- ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
- ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
- ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
- ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl (implements ubic.gemma.core.image.aba.AllenBrainAtlasService)
- ubic.gemma.model.expression.arrayDesign.AlternateName (implements java.io.Serializable)
- 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 (implements java.io.Serializable)
- ubic.gemma.model.analysis.AnalysisResultSet<R> (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet<R>
    - ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild)
- ubic.gemma.rest.AnalysisResultSetsWebService
- ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionServiceImpl (implements ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService)
- ubic.gemma.core.analysis.expression.AnalysisUtilServiceImpl (implements ubic.gemma.core.analysis.expression.AnalysisUtilService)
- ubic.gemma.rest.providers.AnalyticsApplicationEventListener (implements org.glassfish.jersey.server.monitoring.ApplicationEventListener)
- ubic.gemma.rest.providers.AnalyticsRequestEventListener (implements org.glassfish.jersey.server.monitoring.RequestEventListener)
- ubic.gemma.web.util.AnchorTagUtil
- ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
- ubic.gemma.web.controller.expression.experiment.AnnotationController
- ubic.gemma.rest.AnnotationsWebService
- ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
- org.apache.log4j.AppenderSkeleton (implements org.apache.log4j.Appender, org.apache.log4j.spi.OptionHandler)
  - ubic.gemma.core.job.progress.ProgressUpdateAppender
  - ubic.gemma.web.logging.SlackAppender (implements org.apache.log4j.Appender)
- org.springframework.context.support.ApplicationObjectSupport (implements org.springframework.context.ApplicationContextAware)
  - ubic.gemma.web.util.MessageUtilImpl (implements ubic.gemma.web.util.MessageUtil)
  - org.springframework.web.context.support.WebApplicationObjectSupport (implements org.springframework.web.context.ServletContextAware)
    - org.springframework.web.servlet.view.AbstractView (implements org.springframework.beans.factory.BeanNameAware, org.springframework.web.servlet.View)
      - org.springframework.web.servlet.view.feed.AbstractFeedView<T>
        
        org.springframework.web.servlet.view.feed.AbstractRssFeedView
        
        ubic.gemma.web.controller.common.rss.CustomRssViewer
      - ubic.gemma.web.view.TextView
      - ubic.gemma.web.view.XmlView
    - org.springframework.web.servlet.support.WebContentGenerator
      - org.springframework.web.servlet.mvc.AbstractController (implements org.springframework.web.servlet.mvc.Controller)
        
        org.springframework.web.servlet.mvc.AbstractUrlViewController
        
        ubic.gemma.web.controller.common.auditAndSecurity.SystemStatsController
        
        org.springframework.web.servlet.mvc.BaseCommandController
        
        org.springframework.web.servlet.mvc.AbstractFormController
        
        org.springframework.web.servlet.mvc.SimpleFormController
        
        ubic.gemma.web.controller.BaseFormController
        
        ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignFormController
        
        ubic.gemma.web.controller.expression.experiment.ExpressionExperimentFormController
        
        ubic.gemma.web.controller.genome.BlatResultTrackController
        
        ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
- ubic.gemma.rest.util.ArgUtils
- ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
- ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignAddCommand
- ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl (implements ubic.gemma.core.analysis.service.ArrayDesignAnnotationService)
- ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
- ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil
- ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl (implements ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService)
- 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.web.controller.expression.arrayDesign.ArrayDesignProbeMapperController
- ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService)
- ubic.gemma.web.controller.analysis.sequence.ArrayDesignRepeatScanController
- 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.context.AsyncFactoryBeanUtils
- ubic.gemma.core.analysis.report.AuditableObject (implements java.io.Serializable)
- ubic.gemma.core.security.audit.AuditAdvice
- ubic.gemma.web.remote.AuditController
- ubic.gemma.model.common.auditAndSecurity.AuditEvent (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory
- ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService)
- ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType (implements java.io.Serializable)
  - 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.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.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.NotTroubledStatusFlagEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent
  - ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent
  - 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.DataAddedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent
    - 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.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.ProcessedVectorComputationEvent
      - ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent
    - 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.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.VersionedEvent
    - ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent
- ubic.gemma.model.common.auditAndSecurity.AuditTrail (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
- ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy (implements ubic.gemma.rest.analytics.ga4.UserIdRetrievalStrategy)
- gemma.gsec.acl.BaseAclAdvice
  - ubic.gemma.core.security.authorization.acl.AclAdvice
- ubic.gemma.core.config.BaseCodeConfigurer (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
- ubic.gemma.web.controller.BaseController
  - ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
  - ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
  - ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
  - ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController
  - ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController
  - ubic.gemma.web.controller.genome.gene.GeneController
  - ubic.gemma.web.controller.PhenotypeController
  - ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
  - ubic.gemma.web.controller.common.auditAndSecurity.SignupController (implements org.springframework.beans.factory.InitializingBean)
  - ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
- 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.core.datastructure.matrix.BaseExpressionDataMatrix<T> (implements ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>, java.io.Serializable)
  - ubic.gemma.core.datastructure.matrix.EmptyExpressionMatrix
  - ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix
  - ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix
  - ubic.gemma.core.datastructure.matrix.ExpressionDataIntegerMatrix
  - ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix
- 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
- org.directwebremoting.convert.BaseV20Converter (implements org.directwebremoting.extend.Converter)
  - org.directwebremoting.convert.BasicObjectConverter (implements org.directwebremoting.extend.NamedConverter)
    - org.directwebremoting.convert.BeanConverter (implements org.directwebremoting.extend.Converter)
      - ubic.gemma.web.remote.CharacteristicConverter
      - ubic.gemma.web.remote.DoublePointConverter
  - org.directwebremoting.convert.StringConverter (implements org.directwebremoting.extend.Converter)
    - ubic.gemma.web.remote.ClassConverter
    - ubic.gemma.web.remote.DirectionConverter
    - ubic.gemma.web.remote.GOEvidenceCodeConverter
    - ubic.gemma.web.remote.ScaleTypeConverter
    - ubic.gemma.web.remote.StandardQuantitationTypeConverter
- ubic.gemma.model.common.BaseValueObject (implements java.io.Serializable)
- ubic.gemma.core.completion.BashCompletionGenerator (implements ubic.gemma.core.completion.CompletionGenerator)
- 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.expression.arrayDesign.ArrayDesignParser
  - 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 (implements java.io.Serializable)
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
- ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics
- ubic.gemma.web.controller.analysis.preprocess.BatchInfoFetchController
- 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)
- org.springframework.beans.factory.config.BeanDefinitionVisitor
  - ubic.gemma.rest.util.OpenAPIVisitor
- 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.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.model.common.description.BibliographicReference.Factory
- ubic.gemma.model.common.description.BibRefAnnotation (implements java.io.Serializable)
  - ubic.gemma.model.common.description.Keyword
  - ubic.gemma.model.common.description.MedicalSubjectHeading
- ubic.gemma.model.expression.bioAssay.BioAssay.Factory
- ubic.gemma.web.controller.expression.bioAssay.BioAssayController
- ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
- ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.BioAssaySetService)
- ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
- ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
- ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
- ubic.gemma.web.controller.expression.biomaterial.BioMaterialController
- ubic.gemma.model.genome.biosequence.BioSequence.Factory
- ubic.gemma.model.association.BioSequence2GeneProduct (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
  - ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
  - ubic.gemma.model.association.ReferenceAssociation
- ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation.Factory
- ubic.gemma.core.analysis.sequence.BlatAssociationScorer
- ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Factory
- ubic.gemma.core.analysis.sequence.BlatResult2Psl
- ubic.gemma.persistence.initialization.BootstrappedDataSourceFactory (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>)
- ubic.gemma.core.util.BuildInfo (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.rest.util.BuildInfoValueObject
- ubic.gemma.persistence.util.BusinessKey
- ubic.gemma.rest.providers.CacheControlHeaderDecorator (implements javax.ws.rs.ext.WriterInterceptor)
- ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorService)
- io.micrometer.core.instrument.binder.cache.CacheMeterBinder<C> (implements io.micrometer.core.instrument.binder.MeterBinder)
  - ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
- ubic.gemma.web.util.CacheMonitorImpl (implements ubic.gemma.web.util.CacheMonitor, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.persistence.cache.CacheUtils
- ubic.gemma.persistence.util.ChannelUtils
- ubic.gemma.model.common.description.Characteristic.Factory
- ubic.gemma.web.controller.common.CharacteristicBrowserController
- ubic.gemma.persistence.service.common.description.CharacteristicDao.CharacteristicUsageFrequency
- ubic.gemma.model.common.description.CharacteristicUtils
- ubic.gemma.model.genome.Chromosome (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.genome.ChromosomeLocation (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.genome.PhysicalLocation
- ubic.gemma.persistence.service.genome.ChromosomeUtils
- ubic.gemma.model.common.description.CitationValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
- ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution.Factory
- ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.Factory
- ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionCache, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionDao)
- ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand (implements java.io.Serializable)
- ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController
- ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionService)
- ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt (implements java.lang.Comparable<T>)
- ubic.gemma.persistence.util.CommonQueries
- ubic.gemma.web.util.upload.CommonsMultipartFile (implements org.springframework.web.multipart.MultipartFile, java.io.Serializable)
- ubic.gemma.web.util.upload.CommonsMultipartMonitoredResolver (implements org.springframework.web.multipart.MultipartResolver, org.springframework.web.context.ServletContextAware)
- ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy (implements ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy)
- 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.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.model.expression.biomaterial.Compound.Factory
- ubic.gemma.core.config.ConfigurationLinter (implements org.springframework.context.ApplicationListener<E>)
- ubic.gemma.web.util.Constants
- ubic.gemma.model.common.auditAndSecurity.Contact.Factory
- org.springframework.web.context.ContextLoader
  - org.springframework.web.context.ContextLoaderListener (implements javax.servlet.ServletContextListener)
    - ubic.gemma.web.listener.StartupListener
- ubic.gemma.model.analysis.expression.diff.Contrast
- ubic.gemma.model.analysis.expression.diff.ContrastResult (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- 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
- ubic.gemma.web.controller.ControllerUtils
- javax.servlet.http.Cookie (implements java.lang.Cloneable, java.io.Serializable)
  - ubic.gemma.web.util.ConfigurationCookie
- ubic.gemma.persistence.initialization.CreateDatabasePopulator (implements org.springframework.jdbc.datasource.init.DatabasePopulator)
- ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.description.DatabaseEntry (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.description.DatabaseEntry.Factory
- ubic.gemma.core.search.source.DatabaseSearchSource (implements org.springframework.core.Ordered, ubic.gemma.core.search.SearchSource)
- ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl (implements ubic.gemma.core.analysis.report.DatabaseViewGenerator)
- ubic.gemma.core.loader.expression.geo.DatasetCombiner
- ubic.gemma.rest.DatasetsWebService
- ubic.gemma.rest.DatasetsWebService.BatchConfoundValueObject
- ubic.gemma.rest.DatasetsWebService.BatchEffectStatisticsValueObject
- ubic.gemma.rest.DatasetsWebService.BatchInformationValueObject
- ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject (implements ubic.gemma.rest.DatasetsWebService.UsageStatistics)
- ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
- ubic.gemma.rest.DatasetsWebService.SimpleSVDValueObject
- ubic.gemma.core.loader.expression.DataUpdaterImpl (implements ubic.gemma.core.loader.expression.DataUpdater)
- ubic.gemma.model.expression.bioAssayData.DataVector (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
    - ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
    - ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
- ubic.gemma.web.controller.expression.experiment.DEDVController
- ubic.gemma.core.search.DefaultHighlighter (implements ubic.gemma.core.search.lucene.LuceneHighlighter, ubic.gemma.core.search.OntologyHighlighter)
- ubic.gemma.persistence.util.DescribableComparator (implements java.util.Comparator<T>)
- ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject (implements java.io.Serializable)
- ubic.gemma.web.controller.expression.experiment.DesignMatrixRowValueObject.Factory
- org.hibernate.dialect.Dialect (implements org.hibernate.exception.spi.ConversionContext)
  - org.hibernate.dialect.H2Dialect
    - ubic.gemma.persistence.hibernate.H2Dialect
  - org.hibernate.dialect.MySQLDialect
    - org.hibernate.dialect.MySQL5Dialect
      - org.hibernate.dialect.MySQL5InnoDBDialect
        
        org.hibernate.dialect.MySQL57InnoDBDialect
        
        ubic.gemma.persistence.hibernate.MySQL57InnoDBDialect
- ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis.Factory
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig (implements java.io.Serializable)
- ubic.gemma.web.controller.diff.DifferentialExpressionAnalysisController
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService)
- 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.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
- ubic.gemma.web.controller.diff.DifferentialExpressionAnalyzerInfo
- ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService)
- ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence.Factory
- 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.web.controller.diff.DifferentialExpressionSearchController
- ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject (implements java.io.Serializable)
- ubic.gemma.web.controller.diff.DiffExMetaAnalyzerController
- ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService)
- ubic.gemma.web.controller.diff.DiffExpressionSearchCommand (implements java.io.Serializable)
- 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)
- org.apache.commons.fileupload.disk.DiskFileItem (implements org.apache.commons.fileupload.FileItem)
  - ubic.gemma.web.util.upload.MonitoredDiskFileItem
- org.apache.commons.fileupload.disk.DiskFileItemFactory (implements org.apache.commons.fileupload.FileItemFactory)
  - ubic.gemma.web.util.upload.MonitoredDiskFileItemFactory
- 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.model.genome.gene.phenotype.valueObject.DumpsValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.util.EE2CAclQueryUtils
- ubic.gemma.persistence.cache.EhcacheConfig
- ubic.gemma.persistence.cache.EhcacheKeyLock (implements ubic.gemma.persistence.cache.CacheKeyLock)
- ubic.gemma.model.analysis.expression.pca.Eigenvalue (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.pca.Eigenvalue.Factory
- ubic.gemma.model.analysis.expression.pca.Eigenvector (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
- ubic.gemma.core.job.notification.EmailNotificationContext
- ubic.gemma.web.controller.EmptyController
- ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject (implements java.io.Serializable)
- ubic.gemma.web.remote.EntityDelegator<T>
- ubic.gemma.persistence.util.EntityUtils
- ubic.gemma.core.context.EnvironmentProfiles
- ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser
- ubic.gemma.core.loader.entrez.EutilFetch
- ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
- ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject (implements java.io.Serializable)
- ubic.gemma.model.expression.experiment.ExperimentalDesign.Factory
- ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl (implements ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter)
- ubic.gemma.model.expression.experiment.ExperimentalDesignUtils
- ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl (implements ubic.gemma.core.visualization.ExperimentalDesignVisualizationService)
- ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriter
- ubic.gemma.model.association.phenotype.ExperimentalEvidence.Factory
- ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
- ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink (implements java.io.Serializable)
  - ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl
  - ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl
  - ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl
  - ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl
- ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject (implements java.io.Serializable)
- 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.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
- ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil
- ubic.gemma.web.controller.expression.experiment.ExpressionDataFileUploadController
- ubic.gemma.core.analysis.preprocess.ExpressionDataMatrixBuilder
- 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.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.web.controller.expression.experiment.ExpressionExperimentController
- ubic.gemma.web.controller.expression.experiment.ExpressionExperimentDataFetchController
- ubic.gemma.web.controller.expression.experiment.ExpressionExperimentExperimentalFactorValueObject
- ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter
- ubic.gemma.web.controller.expression.experiment.ExpressionExperimentLoadController
- ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService)
- ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCUtils
- ubic.gemma.web.controller.ExpressionExperimentReportGenerationController
- 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.web.controller.expression.experiment.ExpressionExperimentUploadResponse
- ubic.gemma.core.analysis.service.ExpressionExperimentVectorManipulatingService
  - ubic.gemma.core.loader.expression.ExpressionExperimentPlatformSwitchService
  - ubic.gemma.core.analysis.service.OutlierFlaggingServiceImpl (implements ubic.gemma.core.analysis.service.OutlierFlaggingService)
  - ubic.gemma.core.analysis.preprocess.VectorMergingServiceImpl (implements ubic.gemma.core.analysis.preprocess.VectorMergingService)
- ubic.gemma.web.controller.visualization.ExpressionExperimentVisualizationCommand (implements java.io.Serializable)
- ubic.gemma.web.controller.visualization.ExpressionProfileDataObject
- ubic.gemma.model.common.description.ExternalDatabase.Factory
- ubic.gemma.model.common.description.ExternalDatabases
- ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.core.loader.util.parser.ExternalDatabaseUtils
- ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl (implements ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService)
- ubic.gemma.web.controller.visualization.FactorProfile
- ubic.gemma.model.expression.experiment.FactorValue (implements ubic.gemma.model.common.Identifiable, ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
- 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.FactorValueMigratorService.Migration
- ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationResult
- ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService)
- ubic.gemma.core.ontology.FactorValueOntologyService.OntologyStatement
- 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.model.expression.experiment.FactorValueUtils
- ubic.gemma.persistence.util.FactorValueVector
- ubic.gemma.web.feed.FeedReader (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.web.controller.common.auditAndSecurity.FileUpload (implements java.io.Serializable)
- ubic.gemma.web.util.upload.FileUploadUtil
- ubic.gemma.core.util.FileUtils
- ubic.gemma.persistence.util.Filter (implements ubic.gemma.persistence.util.PropertyMapping)
- ubic.gemma.rest.util.args.FilterArg.Filter
- ubic.gemma.rest.util.args.FilterArgBaseListener (implements ubic.gemma.rest.util.args.FilterArgListener)
- ubic.gemma.core.analysis.preprocess.filter.FilterConfig (implements java.io.Serializable)
- ubic.gemma.persistence.util.FilterCriteriaUtils
- 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.completion.FishCompletionGenerator (implements ubic.gemma.core.completion.CompletionGenerator)
- ubic.gemma.model.expression.experiment.Geeq (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.web.controller.common.GemmaClassicHomePageController
- ubic.gemma.core.apps.GemmaCLI
- ubic.gemma.core.config.GemmaRestApiClientConfig
- ubic.gemma.core.util.GemmaRestApiClientImpl (implements ubic.gemma.core.util.GemmaRestApiClient)
- 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, java.io.Serializable)
- ubic.gemma.model.association.Gene2GeneIdAssociation (implements java.io.Serializable)
  - ubic.gemma.model.association.coexpression.Gene2GeneCoexpression (implements java.lang.Comparable<T>)
    - ubic.gemma.model.association.coexpression.HumanGeneCoExpression
      - ubic.gemma.model.association.coexpression.HumanGeneCoExpressionImpl
    - ubic.gemma.model.association.coexpression.MouseGeneCoExpression
      - ubic.gemma.model.association.coexpression.MouseGeneCoExpressionImpl
    - ubic.gemma.model.association.coexpression.OtherGeneCoExpression
      - ubic.gemma.model.association.coexpression.OtherGeneCoExpressionImpl
    - ubic.gemma.model.association.coexpression.RatGeneCoExpression
      - ubic.gemma.model.association.coexpression.RatGeneCoExpressionImpl
- ubic.gemma.model.association.Gene2GOAssociation (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.association.Gene2GOAssociation.Factory
- ubic.gemma.model.genome.gene.GeneAlias (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.genome.gene.GeneAlias.Factory
- ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegree.Factory
- ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl (implements ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService)
- 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 (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 gemma.gsec.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.web.controller.visualization.GeneExpressionProfile
- ubic.gemma.core.analysis.sequence.GeneMappingSummary (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.web.controller.genome.gene.GenePickerController
- ubic.gemma.model.genome.gene.GeneProduct.Factory
- ubic.gemma.web.controller.GeneralSearchController
- ubic.gemma.web.controller.GeneralSearchController.SearchResultValueObject<T>
- ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDao)
- ubic.gemma.model.association.phenotype.GenericEvidence.Factory
- ubic.gemma.model.association.phenotype.GenericExperiment.Factory
- org.springframework.web.filter.GenericFilterBean (implements org.springframework.beans.factory.BeanNameAware, org.springframework.beans.factory.DisposableBean, org.springframework.context.EnvironmentAware, javax.servlet.Filter, org.springframework.beans.factory.InitializingBean, org.springframework.web.context.ServletContextAware)
  - org.springframework.web.filter.OncePerRequestFilter
    - ubic.gemma.rest.servlet.CorsFilter
    - ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
    - ubic.gemma.web.metrics.binder.servlet.ServletMetricsFilter
- ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSearchService)
- ubic.gemma.model.genome.gene.GeneSet.Factory
- ubic.gemma.web.controller.genome.gene.GeneSetController
- ubic.gemma.model.genome.gene.GeneSetMember (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.genome.gene.GeneSetMember.Factory
- 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.web.util.GeneSymbolComparator (implements java.util.Comparator<T>)
- ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl (implements ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.rest.GeneWebService
- ubic.gemma.core.loader.expression.geo.service.GeoBrowser
- ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl (implements org.springframework.beans.factory.DisposableBean, ubic.gemma.core.loader.expression.geo.service.GeoBrowserService, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.core.loader.expression.geo.model.GeoChannel
- 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.web.controller.expression.experiment.GeoRecordBrowserController
- ubic.gemma.core.loader.expression.geo.model.GeoReplication
- ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.geo.model.GeoValues (implements java.io.Serializable)
- ubic.gemma.core.loader.expression.geo.model.GeoVariable
- ubic.gemma.core.goldenpath.GoldenPath (implements java.lang.AutoCloseable)
  - ubic.gemma.core.goldenpath.GoldenPathQuery
  - ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
- ubic.gemma.core.ontology.GoMetricImpl (implements ubic.gemma.core.ontology.GoMetric)
- ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider (implements ubic.gemma.rest.analytics.AnalyticsProvider, org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.model.common.auditAndSecurity.GroupAuthority (implements gemma.gsec.model.GroupAuthority)
  - ubic.gemma.model.common.auditAndSecurity.GroupAuthorityImpl
- ubic.gemma.model.common.auditAndSecurity.GroupAuthority.Factory
- ubic.gemma.rest.providers.GzipHeaderDecorator (implements javax.ws.rs.ext.WriterInterceptor)
- org.springframework.web.servlet.handler.HandlerExceptionResolverComposite (implements org.springframework.web.servlet.HandlerExceptionResolver, org.springframework.core.Ordered)
  - ubic.gemma.web.util.DefaultHandlerExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
- ubic.gemma.core.util.HelpUtils
- 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.web.util.HibernateMonitorImpl (implements ubic.gemma.web.util.HibernateMonitor)
- ubic.gemma.core.search.source.HibernateSearchSource (implements ubic.gemma.core.search.FieldAwareSearchSource, 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.model.analysis.expression.diff.HitListSize (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
- ubic.gemma.web.controller.common.HomePageController
- ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl (implements ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService)
- ubic.gemma.model.association.coexpression.HumanGeneCoExpression.Factory
- ubic.gemma.model.analysis.expression.coexpression.IdArray (implements java.io.Serializable)
  - ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressedGenes
  - ubic.gemma.model.analysis.expression.coexpression.GeneCoexpressionTestedIn
  - ubic.gemma.model.analysis.expression.coexpression.IdArrayValueObject
  - ubic.gemma.model.analysis.expression.coexpression.SupportDetails
    - ubic.gemma.model.analysis.expression.coexpression.HumanCoexpressionSupportDetailsImpl
    - ubic.gemma.model.analysis.expression.coexpression.MouseCoexpressionSupportDetailsImpl
    - ubic.gemma.model.analysis.expression.coexpression.OtherCoexpressionSupportDetailsImpl
    - ubic.gemma.model.analysis.expression.coexpression.RatCoexpressionSupportDetailsImpl
- 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.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
      - ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject (implements ubic.gemma.rest.DatasetsWebService.UsageStatistics)
    - ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject (implements gemma.gsec.model.SecureValueObject)
      - ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
      - ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
        
        ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
      - ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
  - 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.rest.DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject
  - ubic.gemma.model.analysis.AnalysisValueObject<T>
    - ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject (implements java.io.Serializable)
  - ubic.gemma.model.common.description.AnnotationValueObject
    - ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject (implements ubic.gemma.rest.DatasetsWebService.UsageStatistics)
  - ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject
  - ubic.gemma.model.common.description.BibliographicReferenceValueObject
  - 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.common.description.CharacteristicValueObject (implements java.lang.Comparable<T>)
    - ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
  - ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
  - ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
  - ubic.gemma.model.common.description.DatabaseEntryValueObject
    - ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
  - 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.genome.gene.phenotype.valueObject.EvidenceValueObject<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
    - ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject
    - ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject
    - ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject
  - ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
    - ubic.gemma.web.controller.expression.experiment.ExperimentalFactorValueWebUIObject
  - ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject (implements java.lang.Comparable<T>, gemma.gsec.model.SecureValueObject)
    - ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject (implements ubic.gemma.model.common.GemmaSessionBackedValueObject)
      - ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
  - 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 gemma.gsec.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.PhenotypeGroupValueObject
  - ubic.gemma.model.genome.gene.GeneValueObject (implements java.io.Serializable)
    - ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject
  - ubic.gemma.model.common.measurement.MeasurementValueObject
  - ubic.gemma.model.genome.PhysicalLocationValueObject
  - ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
  - ubic.gemma.model.expression.experiment.StatementValueObject (implements java.lang.Comparable<T>)
  - ubic.gemma.model.genome.TaxonValueObject
    - ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject (implements ubic.gemma.rest.DatasetsWebService.UsageStatistics)
- ubic.gemma.core.image.aba.Image
- ubic.gemma.core.image.aba.ImageSeries
- ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject (implements java.io.Serializable)
- ubic.gemma.web.controller.IndexController
- ubic.gemma.core.search.IndexerServiceImpl (implements ubic.gemma.core.search.IndexerService)
- ubic.gemma.rest.util.JacksonConfig
- ubic.gemma.web.util.JavascriptLogger
- ubic.gemma.model.common.auditAndSecurity.JobInfo (implements ubic.gemma.model.common.Identifiable, ubic.gemma.model.common.auditAndSecurity.SecuredNotChild, java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
- ubic.gemma.web.remote.JsonReaderResponse<T>
- com.fasterxml.jackson.databind.JsonSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable)
  - com.fasterxml.jackson.databind.ser.std.StdSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable, com.fasterxml.jackson.databind.jsonschema.SchemaAware, java.io.Serializable)
    - ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer<T>
      - ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer
      - ubic.gemma.rest.serializers.FactorValueValueObjectSerializer
- ubic.gemma.web.view.JSONTableRenderer
- ubic.gemma.web.util.JsonUtil
- ubic.gemma.web.view.JSONView (implements org.springframework.web.servlet.View)
- javax.servlet.jsp.JspContext
  - javax.servlet.jsp.PageContext
    - ubic.gemma.web.taglib.SimplePageContext
- ubic.gemma.model.common.description.Keyword.Factory
- ubic.gemma.web.util.LabelValue (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.core.context.LazyInitByDefaultPostProcessor (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor, org.springframework.core.Ordered)
- ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
- ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig (implements java.io.Serializable)
- ubic.gemma.web.controller.analysis.expression.coexpression.links.LinkAnalysisController
- ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersisterImpl (implements ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister)
- ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisServiceImpl (implements ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService)
- ubic.gemma.persistence.service.association.coexpression.LinkCreator
- ubic.gemma.web.remote.ListBatchCommand
- ubic.gemma.core.util.ListUtils
- ubic.gemma.model.association.phenotype.LiteratureEvidence.Factory
- ubic.gemma.model.common.description.LocalFile (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.description.LocalFile.Factory
- ubic.gemma.persistence.hibernate.LocalSessionFactoryBean (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean, org.springframework.context.ResourceLoaderAware)
- ubic.gemma.core.logging.log4j.Log4jConfigurer (implements ubic.gemma.core.logging.LoggingConfigurer)
- ubic.gemma.core.search.lucene.LuceneQueryUtils
- ubic.gemma.core.util.MailEngineImpl (implements ubic.gemma.core.util.MailEngine)
- ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
- ubic.gemma.core.util.MarkCLIsAsPrototypes (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
- ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation (implements ubic.gemma.model.common.auditAndSecurity.SecuredChild, java.io.Serializable)
- ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
- ubic.gemma.core.analysis.preprocess.MeanVarianceServiceImpl (implements ubic.gemma.core.analysis.preprocess.MeanVarianceService)
- ubic.gemma.model.common.measurement.Measurement (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.measurement.Measurement.Factory
- ubic.gemma.rest.util.MediaTypeUtils
- ubic.gemma.model.common.description.MedicalSubjectHeading.Factory
- ubic.gemma.web.controller.expression.experiment.MetaFile
- 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.web.scheduler.SecureMethodInvokingJobDetailFactoryBean
- ubic.gemma.rest.providers.MetricsApplicationEventListener (implements org.glassfish.jersey.server.monitoring.ApplicationEventListener)
- ubic.gemma.web.util.MinifierPostProcessor (implements net.jawr.web.resource.bundle.postprocess.ResourceBundlePostProcessor)
- ubic.gemma.model.association.coexpression.MouseGeneCoExpression.Factory
- ubic.gemma.model.genome.gene.Multifunctionality (implements java.io.Serializable)
- ubic.gemma.model.genome.gene.Multifunctionality.Factory
- ubic.gemma.core.loader.util.NcbiEntityResolver (implements org.xml.sax.EntityResolver)
- 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.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.web.feed.NewsItem
- ubic.gemma.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink (implements java.lang.Comparable<T>)
- ubic.gemma.rest.providers.ObjectMapperResolver (implements javax.ws.rs.ext.ContextResolver<T>)
- ubic.gemma.web.controller.OntologyController
- 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.OntologyUtils
- ubic.gemma.rest.util.OpenApiConfig
- ubic.gemma.rest.util.OpenApiFactory (implements org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.web.context.ServletConfigAware)
- ubic.gemma.model.association.coexpression.OtherGeneCoExpression.Factory
- ubic.gemma.core.analysis.preprocess.OutlierDetails
- ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl (implements ubic.gemma.core.analysis.preprocess.OutlierDetectionService)
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
  - ubic.gemma.web.util.upload.MonitoredOutputStream
- ubic.gemma.core.loader.util.ParserAndLoaderTools
- ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
- ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService)
- ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication (implements java.io.Serializable)
- ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication.Factory
- ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl (implements ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper)
- ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl (implements ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper)
- ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.model.association.phenotype.PhenotypeMappingType (implements java.lang.Comparable<T>, org.hibernate.usertype.EnhancedUserType, java.io.Serializable)
- ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject (implements java.io.Serializable)
- ubic.gemma.rest.PhenotypeWebService
- ubic.gemma.model.genome.PhysicalLocation.Factory
- ubic.gemma.rest.PlatformsWebService
- ubic.gemma.persistence.util.Pointcuts
- ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
- ubic.gemma.web.controller.analysis.preprocess.PreprocessController
- ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl (implements ubic.gemma.core.analysis.preprocess.PreprocessorService)
- ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis.Factory
- ubic.gemma.model.analysis.expression.pca.ProbeLoading (implements java.io.Serializable)
- 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.core.profiling.ProfilingConfig
- ubic.gemma.core.job.progress.ProgressData (implements java.io.Serializable)
- ubic.gemma.web.job.progress.ProgressStatusServiceImpl (implements ubic.gemma.web.job.progress.ProgressStatusService)
- ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateContext (implements java.lang.AutoCloseable)
- java.beans.PropertyEditorSupport (implements java.beans.PropertyEditor)
  - ubic.gemma.web.propertyeditor.ArrayDesignPropertyEditor
  - ubic.gemma.web.propertyeditor.QuantitationTypePropertyEditor
  - ubic.gemma.web.propertyeditor.SequenceTypePropertyEditor
  - ubic.gemma.web.propertyeditor.TaxonPropertyEditor
- ubic.gemma.persistence.util.PropertyMappingUtils
- ubic.gemma.model.common.protocol.Protocol.Factory
- ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
- ubic.gemma.web.controller.common.description.bibref.PubMedSearchCommand
- ubic.gemma.core.loader.entrez.pubmed.PubMedService
- ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher
- ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser
- ubic.gemma.model.analysis.expression.diff.PvalueDistribution (implements java.io.Serializable)
- ubic.gemma.model.analysis.expression.diff.PvalueDistribution.Factory
- ubic.gemma.core.analysis.preprocess.normalize.QuantileNormalizer<R,C>
- ubic.gemma.model.common.quantitationtype.QuantitationType.Factory
- ubic.gemma.core.loader.expression.geo.QuantitationTypeParameterGuesser
- org.springframework.scheduling.quartz.QuartzJobBean (implements org.quartz.Job)
  - ubic.gemma.web.scheduler.SecureQuartzJobBean
    - ubic.gemma.web.scheduler.Ee2AdUpdateJob (implements org.quartz.StatefulJob)
    - ubic.gemma.web.scheduler.Ee2cUpdateJob (implements org.quartz.StatefulJob)
- ubic.gemma.rest.util.args.QueryArg (implements ubic.gemma.rest.util.args.Arg<T>)
- ubic.gemma.persistence.util.QueryUtils
- ubic.gemma.model.association.coexpression.RatGeneCoExpression.Factory
- ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector.Factory
- ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptcha
- ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaResponse
- org.antlr.v4.runtime.Recognizer<Symbol,ATNInterpreter>
  - org.antlr.v4.runtime.Lexer (implements org.antlr.v4.runtime.TokenSource)
    - ubic.gemma.rest.util.args.FilterArgLexer
  - org.antlr.v4.runtime.Parser
    - ubic.gemma.rest.util.args.FilterArgParser
- 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.core.analysis.sequence.RepeatScan
- ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
- ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy (implements ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy)
- ubic.gemma.rest.providers.RequestExceptionEventListener (implements org.glassfish.jersey.server.monitoring.ApplicationEventListener)
- ubic.gemma.rest.providers.RequestExceptionLogger (implements org.glassfish.jersey.server.monitoring.RequestEventListener)
- ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy (implements ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy)
- ubic.gemma.rest.util.Responders
- ubic.gemma.rest.util.ResponseDataObject<T>
  - ubic.gemma.rest.AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject
  - ubic.gemma.rest.util.FilteredResponseDataObject<T>
    - ubic.gemma.rest.util.FilteredAndLimitedResponseDataObject<T>
      - ubic.gemma.rest.util.QueriedAndFilteredAndLimitedResponseDataObject<T>
        
        ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<T>
    - ubic.gemma.rest.util.QueriedAndFilteredResponseDataObject<T>
      - ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<T>
  - ubic.gemma.rest.util.PaginatedResponseDataObject<T>
    - ubic.gemma.rest.util.FilteredAndPaginatedResponseDataObject<T>
      - ubic.gemma.rest.DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<T>
      - ubic.gemma.rest.util.QueriedAndFilteredAndPaginatedResponseDataObject<T>
        
        ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<T>
        
        ubic.gemma.rest.DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject
  - ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
- ubic.gemma.rest.util.ResponseErrorObject
- ubic.gemma.rest.security.RestAuthEntryPoint (implements org.springframework.security.web.AuthenticationEntryPoint)
- org.springframework.retry.listener.RetryListenerSupport (implements org.springframework.retry.RetryListener)
  - ubic.gemma.persistence.retry.RetryLogger
- ubic.gemma.rest.RootWebService
- ubic.gemma.rest.RootWebService.ApiInfoValueObject
- ubic.gemma.rest.RootWebService.UserValueObject
- ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
- ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
- ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
- ubic.gemma.web.controller.common.rss.RssFeedController
- org.antlr.v4.runtime.RuleContext (implements org.antlr.v4.runtime.tree.RuleNode)
  - org.antlr.v4.runtime.ParserRuleContext
    - ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
    - ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
    - ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
    - ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
    - ubic.gemma.rest.util.args.FilterArgParser.FilterContext
    - ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
    - ubic.gemma.rest.util.args.FilterArgParser.PredicateContext
    - ubic.gemma.rest.util.args.FilterArgParser.QuantifierContext
    - ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
    - ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
- ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService)
- ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix (implements java.io.Serializable)
- ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject (implements java.io.Serializable)
- ubic.gemma.core.search.SearchResult<T> (implements java.lang.Comparable<T>)
- ubic.gemma.core.search.SearchResultDisplayObject (implements java.lang.Comparable<T>)
- ubic.gemma.core.search.SearchServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.search.SearchService)
- ubic.gemma.model.common.search.SearchSettings (implements java.io.Serializable)
- ubic.gemma.core.search.SearchSettingsUtils
- ubic.gemma.model.common.search.SearchSettingsValueObject (implements java.io.Serializable)
- ubic.gemma.rest.SearchWebService
- ubic.gemma.rest.SearchWebService.SearchResultValueObject<T>
- ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
- ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
- ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
- ubic.gemma.core.analysis.sequence.SequenceBinUtils
- ubic.gemma.core.analysis.sequence.SequenceManipulation
- ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  - ubic.gemma.model.genome.sequenceAnalysis.BlatResult
- ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject (implements java.io.Serializable)
- ubic.gemma.core.analysis.sequence.SequenceWriter
- 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)
- javax.servlet.ServletRequestWrapper (implements javax.servlet.ServletRequest)
  - javax.servlet.http.HttpServletRequestWrapper (implements javax.servlet.http.HttpServletRequest)
    - org.springframework.web.multipart.support.AbstractMultipartHttpServletRequest (implements org.springframework.web.multipart.MultipartHttpServletRequest)
      - ubic.gemma.web.util.upload.FailedMultipartHttpServletRequest
- ubic.gemma.web.persistence.SessionListManagerImpl (implements ubic.gemma.web.persistence.SessionListManager)
- ubic.gemma.core.config.Settings
- ubic.gemma.core.config.SettingsConfig
- ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
- ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
- ubic.gemma.core.analysis.sequence.ShellDelegatingBlat (implements ubic.gemma.core.analysis.sequence.Blat)
- ubic.gemma.web.controller.common.auditAndSecurity.SidValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl (implements ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService)
- ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentCommandValidation
- ubic.gemma.core.loader.genome.SimpleFastaCmd (implements ubic.gemma.core.loader.genome.FastaCmd)
- ubic.gemma.core.search.lucene.SimpleHTMLFormatter (implements org.apache.lucene.search.highlight.Formatter)
- ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp
- ubic.gemma.core.search.lucene.SimpleMarkdownFormatter (implements org.apache.lucene.search.highlight.Formatter)
- ubic.gemma.core.util.SimpleThreadFactory (implements java.util.concurrent.ThreadFactory)
- ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.persistence.util.Sort (implements ubic.gemma.persistence.util.PropertyMapping)
- ubic.gemma.rest.util.args.SortArg.Sort
- ubic.gemma.rest.util.SortValueObject
- ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl (implements ubic.gemma.core.analysis.preprocess.SplitExperimentService)
- ubic.gemma.core.context.SpringContextUtils
- ubic.gemma.model.expression.experiment.Statement.Factory
- ubic.gemma.persistence.cache.StaticCacheKeyLock (implements ubic.gemma.persistence.cache.CacheKeyLock)
- ubic.gemma.core.profiling.StopWatchUtils
- ubic.gemma.core.profiling.StopWatchUtils.StopWatchRegion (implements java.lang.AutoCloseable)
- ubic.gemma.web.remote.StringPoint
- ubic.gemma.core.job.SubmittedTasksMaintenance
- ubic.gemma.core.job.progress.SubmittedTaskValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.util.Subquery
- ubic.gemma.persistence.util.Subquery.Alias
- ubic.gemma.persistence.util.SubqueryUtils
- ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException.SuspiciousValueResult
- ubic.gemma.web.controller.analysis.preprocess.SvdController
- ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl (implements ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper)
- ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl (implements ubic.gemma.core.analysis.preprocess.svd.SVDService)
- ubic.gemma.core.analysis.preprocess.svd.SVDValueObject (implements java.io.Serializable)
- ubic.gemma.web.controller.monitoring.SystemMonitorController
- ubic.gemma.persistence.service.maintenance.TableMaintenanceUtilImpl (implements ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil)
- javax.servlet.jsp.tagext.TagExtraInfo
  - ubic.gemma.web.taglib.ConstantsTei
- javax.servlet.jsp.tagext.TagSupport (implements javax.servlet.jsp.tagext.IterationTag, java.io.Serializable)
  - ubic.gemma.web.taglib.arrayDesign.ArrayDesignGroupingTag
  - ubic.gemma.web.taglib.expression.experiment.AssayViewTag
  - ubic.gemma.web.taglib.ConstantsTag
  - ubic.gemma.web.taglib.DatabaseEntryTag
  - ubic.gemma.web.taglib.common.auditAndSecurity.ExceptionTag
  - ubic.gemma.web.taglib.expression.experiment.ExperimentQCTag
  - ubic.gemma.web.taglib.ShortBibliographicReferenceTag
- ubic.gemma.core.job.TaskCommand (implements java.io.Serializable)
  - ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
  - ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
  - ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
  - ubic.gemma.web.controller.coexpressionSearch.CoexSearchTaskCommand
  - 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.web.controller.expression.experiment.ExpressionExperimentDataFetchCommand
  - ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand
  - ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand
    - ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand
  - ubic.gemma.core.tasks.maintenance.IndexerTaskCommand
  - ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskCommand
  - ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand
  - ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetaData
    - ubic.gemma.web.controller.expression.experiment.SimpleExpressionExperimentLoadTaskCommand
  - 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.web.controller.TaskCompletionController
- 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.rest.TaxaWebService
- ubic.gemma.model.genome.Taxon (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.genome.Taxon.Factory
- ubic.gemma.core.loader.genome.taxon.TaxonLoader
- ubic.gemma.persistence.service.genome.taxon.TaxonUtils
- ubic.gemma.core.ontology.jena.TGFVO
- java.lang.Thread (implements java.lang.Runnable)
  - ubic.gemma.core.util.concurrent.GenericStreamConsumer
  - ubic.gemma.core.util.concurrent.ParsingStreamConsumer<T>
- 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)
- java.lang.Throwable (implements java.io.Serializable)
  - java.lang.Exception
    - ubic.gemma.rest.util.EntityNotFoundException
    - ubic.gemma.core.loader.entrez.pubmed.ESearchException
    - java.io.IOException
      - ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry
    - ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException
    - ubic.gemma.core.datastructure.matrix.QuantitationMismatchException
      - ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException
      - ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException
    - java.lang.RuntimeException
      - ubic.gemma.core.loader.util.AlreadyExistsInSystemException
      - ubic.gemma.core.association.phenotype.EntityNotFoundException
      - ubic.gemma.web.util.EntityNotFoundException
      - ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException
      - ubic.gemma.core.loader.util.parser.FileFormatException
      - ubic.gemma.core.util.GemmaRestApiClientException
      - 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.FailedToComputeSingularValueDecomposition
        
        ubic.gemma.core.analysis.preprocess.filter.FilteringException
        
        ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException
        
        ubic.gemma.core.analysis.preprocess.InsufficientProbesException
        
        ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException
        
        ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException
        
        ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException
        
        ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
      - ubic.gemma.core.datastructure.matrix.QuantitationTypeConversionException
        
        ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException
      - ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
      - ubic.gemma.web.util.ServiceUnavailableException
      - ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException
      - javax.ws.rs.WebApplicationException
        
        javax.ws.rs.ClientErrorException
        
        javax.ws.rs.BadRequestException
        
        ubic.gemma.rest.util.MalformedArgException
    - 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
- org.springframework.xml.transform.TransformerObjectSupport
  - org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint (implements org.springframework.ws.server.endpoint.PayloadEndpoint)
    - ubic.gemma.web.services.AbstractGemmaEndpoint
      - ubic.gemma.web.services.ArrayDesignIdentifierByNameEndpoint
      - ubic.gemma.web.services.ArrayDesignUsedEndpoint
      - ubic.gemma.web.services.DEDVfromEEIDGeneIDEndpoint
      - ubic.gemma.web.services.DEDVRankEndpoint
      - ubic.gemma.web.services.DifferentialExpressionProbeResultEndpoint
      - ubic.gemma.web.services.ExperimentAnnotationEndpoint
      - ubic.gemma.web.services.ExperimentDEDVEndpoint
      - ubic.gemma.web.services.ExperimentIDbyTaxonEndpoint
      - ubic.gemma.web.services.ExperimentIdEndpoint
      - ubic.gemma.web.services.ExperimentNameEndpoint
      - ubic.gemma.web.services.ExperimentNumSamplesEndpoint
      - ubic.gemma.web.services.ExpressionExperimentSetIDsEndpoint
      - ubic.gemma.web.services.Gene2GOdescriptionEndpoint
      - ubic.gemma.web.services.Gene2GoTermEndpoint
      - ubic.gemma.web.services.Gene2ProbeEndpoint
      - ubic.gemma.web.services.GeneByNCBIIdEndpoint
      - ubic.gemma.web.services.GeneCoexpressionEndpoint
      - ubic.gemma.web.services.GeneCoexpressionSearchEndpoint
      - ubic.gemma.web.services.GeneDetailsByGeneIDEndpoint
      - ubic.gemma.web.services.GeneIDbyTaxonEndpoint
      - ubic.gemma.web.services.GeneIdEndpoint
      - ubic.gemma.web.services.GeneNameEndpoint
      - ubic.gemma.web.services.GeneOverlapEndpoint
      - ubic.gemma.web.services.GoTerm2GeneEndpoint
      - ubic.gemma.web.services.Probe2GeneEndpoint
- ubic.gemma.model.expression.biomaterial.Treatment.Factory
- ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController
- ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl (implements ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues)
- ubic.gemma.web.util.UnhandledExceptionResolver (implements org.springframework.web.servlet.HandlerExceptionResolver)
- ubic.gemma.model.common.measurement.Unit (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
- ubic.gemma.model.common.measurement.Unit.Factory
- ubic.gemma.web.util.upload.UploadInfo (implements java.io.Serializable)
- ubic.gemma.web.util.upload.UploadListener (implements ubic.gemma.web.util.upload.OutputStreamListener)
- ubic.gemma.model.common.auditAndSecurity.User.Factory
- ubic.gemma.web.listener.UserCounterListener (implements javax.servlet.http.HttpSessionListener, javax.servlet.ServletContextListener)
- ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
- ubic.gemma.web.controller.common.auditAndSecurity.UserGroupValueObject
- ubic.gemma.web.controller.common.auditAndSecurity.UserListController
- ubic.gemma.core.security.authentication.UserManagerImpl (implements ubic.gemma.core.security.authentication.UserManager)
- ubic.gemma.model.common.auditAndSecurity.UserQuery (implements ubic.gemma.model.common.auditAndSecurity.SecuredNotChild, java.io.Serializable)
- ubic.gemma.model.common.auditAndSecurity.UserQuery.Factory
- ubic.gemma.core.security.authentication.UserServiceImpl (implements ubic.gemma.core.security.authentication.UserService)
- ubic.gemma.web.listener.UserTracker
- ubic.gemma.web.controller.common.auditAndSecurity.UserUpdateCommand
- ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject
- ubic.gemma.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject (implements java.io.Serializable)
- ubic.gemma.persistence.util.ValueObjectConfig
- ubic.gemma.web.controller.visualization.VisualizationValueObject
- ubic.gemma.web.controller.WebConstants
- ubic.gemma.rest.util.WellComposedErrorBody
- ubic.gemma.core.analysis.report.WhatsNew
- ubic.gemma.web.controller.common.auditAndSecurity.WhatsNewController
- ubic.gemma.core.analysis.report.WhatsNewServiceImpl (implements ubic.gemma.core.analysis.report.WhatsNewService)
- ubic.gemma.core.util.XMLUtils

Interface Hierarchy

ubic.gemma.core.image.aba.AllenBrainAtlasService
ubic.gemma.core.analysis.expression.AnalysisUtilService
ubic.gemma.rest.analytics.AnalyticsProvider
ubic.gemma.rest.util.args.Arg<T>
ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
ubic.gemma.core.analysis.report.ArrayDesignReportService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
java.lang.AutoCloseable
- ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition
org.springframework.beans.factory.Aware
- org.springframework.context.ApplicationContextAware
  - ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
ubic.gemma.persistence.service.BaseDao<T>
- ubic.gemma.persistence.service.analysis.AnalysisDao<T>
  - ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao<T>
    - ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao
    - 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.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.association.coexpression.CoexpressionNodeDegreeDao
- ubic.gemma.persistence.service.expression.biomaterial.CompoundDao
- ubic.gemma.persistence.service.common.auditAndSecurity.ContactDao
- 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.association.phenotype.DifferentialExpressionEvidenceDao
- ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
- ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao
- ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDao
- 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.association.phenotype.GenericEvidenceDao
- ubic.gemma.persistence.service.association.phenotype.GenericExperimentDao
- ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDao
- ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao
- ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
- ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
- ubic.gemma.persistence.service.common.protocol.ProtocolDao
- ubic.gemma.persistence.service.association.ReferenceAssociationDao
- ubic.gemma.persistence.service.expression.experiment.StatementDao
- 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.analysis.AnalysisService<T>
    - ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
    - ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>
      - ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService (also extends ubic.gemma.persistence.service.BaseService<O>)
      - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
  - ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
  - ubic.gemma.persistence.service.BaseService<O>
    - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - 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.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>)
    - ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
    - ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>)
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
    - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
    - ubic.gemma.persistence.service.common.description.ExternalDatabaseService
    - ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<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.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - 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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (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.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.genome.sequenceAnalysis.BlatAssociationService
  - 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.association.phenotype.service.PhenotypeAssociationService
  - ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
  - ubic.gemma.persistence.service.common.protocol.ProtocolService
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService<C> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService<C>)
    - 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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
- ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>
  - ubic.gemma.persistence.service.common.description.BibliographicReferenceService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
  - ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
  - ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.genome.biosequence.BioSequenceService (also extends ubic.gemma.persistence.service.BaseService<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.BaseService<O>)
  - ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.FilteringService<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.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.BaseService<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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.expression.experiment.GeeqService
  - ubic.gemma.persistence.service.genome.gene.GeneProductService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.BaseService<O>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService<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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
- ubic.gemma.persistence.service.expression.experiment.BioAssaySetService
- ubic.gemma.persistence.service.genome.ChromosomeService
- ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorService<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.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.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.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.BaseService<O>)
    - ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.BaseService<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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
    - ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.BaseService<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.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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService<C,VO>)
  - ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService<C,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    - 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.experiment.ExpressionExperimentService (also extends ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService<C>)
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService
ubic.gemma.core.analysis.sequence.Blat
ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorService
ubic.gemma.persistence.cache.CacheKeyLock
ubic.gemma.web.util.CacheMonitor
java.util.concurrent.Callable<V>
- ubic.gemma.core.job.Task<C>
  - ubic.gemma.web.tasks.analysis.sequence.ArrayDesignRepeatScanTask
  - 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.maintenance.ExpressionExperimentReportTask
  - ubic.gemma.core.tasks.maintenance.IndexerTask
  - ubic.gemma.core.tasks.analysis.expression.PreprocessExperimentTask
  - ubic.gemma.core.tasks.analysis.expression.SvdTask
ubic.gemma.core.util.CLI
ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy
ubic.gemma.persistence.service.association.coexpression.CoexpressionCache
ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
ubic.gemma.persistence.service.association.coexpression.CoexpressionService
ubic.gemma.core.completion.CompletionGenerator
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.core.analysis.report.DatabaseViewGenerator
ubic.gemma.rest.DatasetsWebService.UsageStatistics
ubic.gemma.core.loader.expression.DataUpdater
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
ubic.gemma.rest.util.args.EntityArgService<T,S>
ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter
ubic.gemma.core.visualization.ExperimentalDesignVisualizationService
ubic.gemma.core.loader.expression.ExperimentPlatformSwitchHelperService
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix<T>
ubic.gemma.core.analysis.service.ExpressionDataMatrixService
ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionService
ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService
ubic.gemma.core.analysis.report.ExpressionExperimentReportService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper
ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion
ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService
ubic.gemma.core.ontology.FactorValueOntologyService
ubic.gemma.core.ontology.FactorValueOntologyUtils.StatementVisitor<U,E>
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.loader.util.fetcher.HttpArchiveFetcherInterface
ubic.gemma.core.analysis.service.FileService<T>
- ubic.gemma.core.analysis.service.JsonFileService<T>
- ubic.gemma.core.analysis.service.TsvFileService<T>
  - ubic.gemma.core.analysis.service.DifferentialExpressionAnalysisResultListFileService
  - ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService
  - ubic.gemma.core.analysis.service.ExpressionDataFileService
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.core.analysis.expression.coexpression.GeneCoexpressionSearchService
ubic.gemma.persistence.service.genome.gene.GeneCoreService
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.GeneSearchService
ubic.gemma.core.search.GeneSetSearch
ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
ubic.gemma.core.loader.expression.geo.service.GeoBrowserService
ubic.gemma.core.loader.expression.geo.service.GeoService
ubic.gemma.core.search.getOntologyTermFormatter
ubic.gemma.core.ontology.GoMetric
org.springframework.security.provisioning.GroupManager
- gemma.gsec.authentication.UserManager (also extends org.springframework.security.provisioning.UserDetailsManager)
  - ubic.gemma.core.security.authentication.UserManager
ubic.gemma.web.util.HibernateMonitor
ubic.gemma.core.search.Highlighter
- ubic.gemma.core.search.lucene.LuceneHighlighter
- ubic.gemma.core.search.OntologyHighlighter
ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
ubic.gemma.model.common.Identifiable
- ubic.gemma.model.common.Describable
- ubic.gemma.model.common.auditAndSecurity.Securable (also extends gemma.gsec.model.Securable)
  - ubic.gemma.model.common.auditAndSecurity.Auditable
    - ubic.gemma.model.common.auditAndSecurity.curation.Curatable
  - ubic.gemma.model.common.auditAndSecurity.SecuredChild (also extends gemma.gsec.model.SecuredChild)
  - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends gemma.gsec.model.SecuredNotChild)
ubic.gemma.core.search.IndexerService
ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister
ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService
ubic.gemma.core.logging.LoggingConfigurer
ubic.gemma.core.util.MailEngine
ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
ubic.gemma.core.analysis.preprocess.MeanVarianceService
ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
ubic.gemma.web.util.MessageUtil
io.micrometer.core.instrument.binder.MeterBinder
- ubic.gemma.core.job.TaskRunningService
ubic.basecode.ontology.providers.OntologyService
- ubic.gemma.core.ontology.providers.GeneOntologyService
ubic.gemma.core.ontology.OntologyService
ubic.gemma.core.analysis.preprocess.OutlierDetectionService
ubic.gemma.core.analysis.service.OutlierFlaggingService
ubic.gemma.web.util.upload.OutputStreamListener
ubic.gemma.core.loader.util.parser.Parser<T>
- ubic.gemma.core.loader.util.parser.LineParser<T>
org.antlr.v4.runtime.tree.ParseTreeListener
- ubic.gemma.rest.util.args.FilterArgListener
ubic.gemma.persistence.persister.Persister
- ubic.gemma.persistence.persister.PersisterHelper
ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService
ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper
ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper
ubic.gemma.core.analysis.preprocess.PreprocessorService
ubic.gemma.core.analysis.sequence.ProbeMapper
ubic.gemma.web.job.progress.ProgressStatusService
ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateCallback
ubic.gemma.persistence.util.PropertyMapping
ubic.gemma.core.loader.util.QueuingParser<T>
ubic.gemma.rest.util.Responders.FilterMethod<T>
ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService
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
java.io.Serializable
- org.hibernate.transform.ResultTransformer
  - ubic.gemma.persistence.hibernate.TypedResultTransformer<T>
- gemma.gsec.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 (also extends gemma.gsec.model.SecuredChild)
    - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends gemma.gsec.model.SecuredNotChild)
  - gemma.gsec.model.SecuredChild
    - ubic.gemma.model.common.auditAndSecurity.SecuredChild (also extends ubic.gemma.model.common.auditAndSecurity.Securable)
  - gemma.gsec.model.SecuredNotChild
    - ubic.gemma.model.common.auditAndSecurity.SecuredNotChild (also extends ubic.gemma.model.common.auditAndSecurity.Securable)
ubic.gemma.web.persistence.SessionListManager
ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
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.core.analysis.preprocess.svd.SVDServiceHelper
ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
ubic.gemma.core.job.notification.TaskMailUtils
ubic.gemma.core.job.notification.TaskPostProcessing
ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService
ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
org.springframework.security.core.userdetails.UserDetailsService
- org.springframework.security.provisioning.UserDetailsManager
  - gemma.gsec.authentication.UserManager (also extends org.springframework.security.provisioning.GroupManager)
    - ubic.gemma.core.security.authentication.UserManager
ubic.gemma.rest.analytics.ga4.UserIdRetrievalStrategy
gemma.gsec.authentication.UserService
- ubic.gemma.core.security.authentication.UserService
ubic.gemma.core.analysis.preprocess.VectorMergingService
ubic.gemma.model.common.description.Versioned
ubic.gemma.core.analysis.report.WhatsNewService

Annotation Type Hierarchy

ubic.gemma.rest.annotations.CacheControl (implements java.lang.annotation.Annotation)
ubic.gemma.rest.annotations.CacheControls (implements java.lang.annotation.Annotation)
ubic.gemma.model.annotations.GemmaRestOnly (implements java.lang.annotation.Annotation)
ubic.gemma.model.annotations.GemmaWebOnly (implements java.lang.annotation.Annotation)
ubic.gemma.rest.annotations.GZIP (implements java.lang.annotation.Annotation)
ubic.gemma.core.security.audit.IgnoreAudit (implements java.lang.annotation.Annotation)
ubic.gemma.persistence.retry.Retryable (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)

Enum Hierarchy

java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
  - ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
  - ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
  - ubic.gemma.model.common.auditAndSecurity.AuditAction
  - ubic.gemma.model.expression.experiment.BatchEffectType
  - ubic.gemma.model.common.description.DatabaseType
  - ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
  - ubic.gemma.model.analysis.expression.diff.Direction
  - ubic.gemma.core.loader.entrez.EutilFetch.Mode
  - ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType
  - ubic.gemma.model.expression.experiment.FactorType
  - ubic.gemma.persistence.util.Filter.Operator
  - ubic.gemma.persistence.service.expression.experiment.GeeqService.ScoreMode
  - ubic.gemma.core.apps.GemmaCLI.CommandGroup
  - ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
  - ubic.gemma.model.common.quantitationtype.GeneralType
  - 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.model.GeoReplication.ReplicationType
  - ubic.gemma.core.loader.expression.geo.model.GeoSample.LibraryStrategy
  - ubic.gemma.core.loader.expression.geo.model.GeoSeries.SeriesType
  - ubic.gemma.core.loader.expression.geo.model.GeoVariable.VariableType
  - ubic.gemma.model.association.GOEvidenceCode
  - ubic.gemma.core.ontology.GoMetric.Metric
  - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
  - ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold
  - ubic.gemma.model.common.measurement.MeasurementKind
  - ubic.gemma.model.common.measurement.MeasurementType
  - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
  - ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
  - ubic.gemma.model.genome.biosequence.PolymerType
  - ubic.gemma.model.common.quantitationtype.PrimitiveType
  - ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
  - ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
  - ubic.gemma.model.common.quantitationtype.ScaleType
  - ubic.gemma.model.common.search.SearchSettings.SearchMode
  - ubic.gemma.model.genome.biosequence.SequenceType
  - ubic.gemma.core.analysis.sequence.ShellDelegatingBlat.BlattableGenome
  - ubic.gemma.persistence.util.Sort.Direction
  - ubic.gemma.rest.util.args.SortArg.Sort.Direction
  - 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.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod

Hierarchy For All Packages

Class Hierarchy

Interface Hierarchy

Annotation Type Hierarchy

Enum Hierarchy