Hierarchy For All Packages

Package Hierarchies:

• ubic.gemma.core.analysis.expression,
• ubic.gemma.core.analysis.expression.coexpression,
• ubic.gemma.core.analysis.expression.coexpression.links,
• ubic.gemma.core.analysis.expression.diff,
• ubic.gemma.core.analysis.preprocess,
• ubic.gemma.core.analysis.preprocess.batcheffects,
• ubic.gemma.core.analysis.preprocess.filter,
• ubic.gemma.core.analysis.preprocess.normalize,
• ubic.gemma.core.analysis.preprocess.svd,
• ubic.gemma.core.analysis.report,
• ubic.gemma.core.analysis.sequence,
• ubic.gemma.core.analysis.service,
• ubic.gemma.core.analysis.util,
• ubic.gemma.core.annotation.reference,
• ubic.gemma.core.apps,
• ubic.gemma.core.association.phenotype,
• ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence,
• ubic.gemma.core.datastructure.matrix,
• ubic.gemma.core.expression.experiment,
• ubic.gemma.core.expression.experiment.service,
• ubic.gemma.core.externalDb,
• ubic.gemma.core.genome.gene,
• ubic.gemma.core.genome.gene.service,
• ubic.gemma.core.image,
• ubic.gemma.core.image.aba,
• ubic.gemma.core.job,
• ubic.gemma.core.job.executor.common,
• ubic.gemma.core.job.executor.webapp,
• ubic.gemma.core.job.progress,
• ubic.gemma.core.loader.association,
• ubic.gemma.core.loader.association.phenotype,
• ubic.gemma.core.loader.entrez,
• ubic.gemma.core.loader.entrez.pubmed,
• ubic.gemma.core.loader.expression,
• ubic.gemma.core.loader.expression.arrayDesign,
• ubic.gemma.core.loader.expression.arrayExpress,
• ubic.gemma.core.loader.expression.arrayExpress.util,
• ubic.gemma.core.loader.expression.geo,
• ubic.gemma.core.loader.expression.geo.fetcher,
• ubic.gemma.core.loader.expression.geo.model,
• ubic.gemma.core.loader.expression.geo.service,
• ubic.gemma.core.loader.expression.geo.util,
• ubic.gemma.core.loader.expression.simple,
• ubic.gemma.core.loader.expression.simple.model,
• ubic.gemma.core.loader.genome,
• ubic.gemma.core.loader.genome.gene,
• ubic.gemma.core.loader.genome.gene.ncbi,
• ubic.gemma.core.loader.genome.gene.ncbi.homology,
• ubic.gemma.core.loader.genome.gene.ncbi.model,
• ubic.gemma.core.loader.genome.taxon,
• ubic.gemma.core.loader.util,
• ubic.gemma.core.loader.util.biomart,
• ubic.gemma.core.loader.util.converter,
• ubic.gemma.core.loader.util.fetcher,
• ubic.gemma.core.loader.util.parser,
• ubic.gemma.core.loader.util.sdo,
• ubic.gemma.core.ontology,
• ubic.gemma.core.ontology.providers,
• ubic.gemma.core.search,
• ubic.gemma.core.search.indexer,
• ubic.gemma.core.search.source,
• ubic.gemma.core.security.audit,
• ubic.gemma.core.security.authentication,
• ubic.gemma.core.security.authorization.acl,
• ubic.gemma.core.tasks,
• ubic.gemma.core.tasks.analysis.coexp,
• ubic.gemma.core.tasks.analysis.diffex,
• ubic.gemma.core.tasks.analysis.expression,
• ubic.gemma.core.tasks.analysis.sequence,
• ubic.gemma.core.tasks.maintenance,
• ubic.gemma.core.tasks.visualization,
• ubic.gemma.core.util,
• ubic.gemma.core.util.concurrent,
• ubic.gemma.core.visualization,
• ubic.gemma.model,
• ubic.gemma.model.analysis,
• ubic.gemma.model.analysis.expression,
• ubic.gemma.model.analysis.expression.coexpression,
• ubic.gemma.model.analysis.expression.diff,
• ubic.gemma.model.analysis.expression.pca,
• ubic.gemma.model.annotations,
• ubic.gemma.model.association,
• ubic.gemma.model.association.coexpression,
• ubic.gemma.model.association.phenotype,
• ubic.gemma.model.common,
• ubic.gemma.model.common.auditAndSecurity,
• ubic.gemma.model.common.auditAndSecurity.curation,
• ubic.gemma.model.common.auditAndSecurity.eventType,
• ubic.gemma.model.common.description,
• ubic.gemma.model.common.measurement,
• ubic.gemma.model.common.protocol,
• ubic.gemma.model.common.quantitationtype,
• ubic.gemma.model.common.search,
• ubic.gemma.model.expression,
• ubic.gemma.model.expression.arrayDesign,
• ubic.gemma.model.expression.bioAssay,
• ubic.gemma.model.expression.bioAssayData,
• ubic.gemma.model.expression.biomaterial,
• ubic.gemma.model.expression.designElement,
• ubic.gemma.model.expression.experiment,
• ubic.gemma.model.genome,
• ubic.gemma.model.genome.biosequence,
• ubic.gemma.model.genome.gene,
• ubic.gemma.model.genome.gene.phenotype,
• ubic.gemma.model.genome.gene.phenotype.valueObject,
• ubic.gemma.model.genome.sequenceAnalysis,
• ubic.gemma.persistence.model,
• ubic.gemma.persistence.model.usertypes,
• ubic.gemma.persistence.persister,
• ubic.gemma.persistence.retry,
• ubic.gemma.persistence.service,
• ubic.gemma.persistence.service.analysis,
• ubic.gemma.persistence.service.analysis.expression,
• ubic.gemma.persistence.service.analysis.expression.coexpression,
• ubic.gemma.persistence.service.analysis.expression.diff,
• ubic.gemma.persistence.service.analysis.expression.pca,
• ubic.gemma.persistence.service.analysis.expression.sampleCoexpression,
• ubic.gemma.persistence.service.association,
• ubic.gemma.persistence.service.association.coexpression,
• ubic.gemma.persistence.service.association.phenotype,
• ubic.gemma.persistence.service.association.phenotype.service,
• ubic.gemma.persistence.service.common,
• ubic.gemma.persistence.service.common.auditAndSecurity,
• ubic.gemma.persistence.service.common.auditAndSecurity.curation,
• ubic.gemma.persistence.service.common.description,
• ubic.gemma.persistence.service.common.measurement,
• ubic.gemma.persistence.service.common.protocol,
• ubic.gemma.persistence.service.common.quantitationtype,
• ubic.gemma.persistence.service.expression.arrayDesign,
• ubic.gemma.persistence.service.expression.bioAssay,
• ubic.gemma.persistence.service.expression.bioAssayData,
• ubic.gemma.persistence.service.expression.biomaterial,
• ubic.gemma.persistence.service.expression.designElement,
• ubic.gemma.persistence.service.expression.experiment,
• ubic.gemma.persistence.service.genome,
• ubic.gemma.persistence.service.genome.biosequence,
• ubic.gemma.persistence.service.genome.gene,
• ubic.gemma.persistence.service.genome.sequenceAnalysis,
• ubic.gemma.persistence.service.genome.taxon,
• ubic.gemma.persistence.util,
• ubic.gemma.persistence.util.monitor,
• ubic.gemma.web.controller,
• ubic.gemma.web.controller.analysis.expression.coexpression.links,
• ubic.gemma.web.controller.analysis.preprocess,
• ubic.gemma.web.controller.analysis.sequence,
• ubic.gemma.web.controller.coexpressionSearch,
• ubic.gemma.web.controller.common,
• ubic.gemma.web.controller.common.auditAndSecurity,
• ubic.gemma.web.controller.common.auditAndSecurity.recaptcha,
• ubic.gemma.web.controller.common.description.bibref,
• ubic.gemma.web.controller.common.rss,
• ubic.gemma.web.controller.diff,
• ubic.gemma.web.controller.expression.arrayDesign,
• ubic.gemma.web.controller.expression.bioAssay,
• ubic.gemma.web.controller.expression.biomaterial,
• ubic.gemma.web.controller.expression.designElement,
• ubic.gemma.web.controller.expression.experiment,
• ubic.gemma.web.controller.genome,
• ubic.gemma.web.controller.genome.gene,
• ubic.gemma.web.controller.monitoring,
• ubic.gemma.web.controller.visualization,
• ubic.gemma.web.feed,
• ubic.gemma.web.job.progress,
• ubic.gemma.web.listener,
• ubic.gemma.web.logging,
• ubic.gemma.web.persistence,
• ubic.gemma.web.propertyeditor,
• ubic.gemma.web.remote,
• ubic.gemma.web.scheduler,
• ubic.gemma.web.services,
• ubic.gemma.web.services.rest,
• ubic.gemma.web.services.rest.annotations,
• ubic.gemma.web.services.rest.providers,
• ubic.gemma.web.services.rest.security,
• ubic.gemma.web.services.rest.servlet,
• ubic.gemma.web.services.rest.swagger,
• ubic.gemma.web.services.rest.swagger.resolvers,
• ubic.gemma.web.services.rest.util,
• ubic.gemma.web.services.rest.util.args,
• ubic.gemma.web.taglib,
• ubic.gemma.web.taglib.arrayDesign,
• ubic.gemma.web.taglib.common.auditAndSecurity,
• ubic.gemma.web.taglib.expression.experiment,
• ubic.gemma.web.tasks.analysis.sequence,
• ubic.gemma.web.util,
• ubic.gemma.web.util.upload,
• ubic.gemma.web.view

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)
    • gemma.gsec.acl.afterinvocation.ByAssociationFilteringProvider<T,A>
      • ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
      • ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
  • 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
  • ubic.gemma.web.services.rest.util.args.AbstractArg<T> (implements ubic.gemma.web.services.rest.util.args.Arg<T>)
    • ubic.gemma.web.services.rest.util.args.AbstractArrayArg<T>
      • ubic.gemma.web.services.rest.util.args.AbstractEntityArrayArg<A,O,S>
        • ubic.gemma.web.services.rest.util.args.CompositeSequenceArrayArg
        • ubic.gemma.web.services.rest.util.args.DatabaseEntryArrayArg
        • ubic.gemma.web.services.rest.util.args.DatasetArrayArg
        • ubic.gemma.web.services.rest.util.args.FactorValueArrayArg
        • ubic.gemma.web.services.rest.util.args.GeneArrayArg
        • ubic.gemma.web.services.rest.util.args.PlatformArrayArg
        • ubic.gemma.web.services.rest.util.args.TaxonArrayArg
      • ubic.gemma.web.services.rest.util.args.StringArrayArg
    • ubic.gemma.web.services.rest.util.args.AbstractEntityArg<T,O,S>
      • ubic.gemma.web.services.rest.util.args.CompositeSequenceArg<T>
        • ubic.gemma.web.services.rest.util.args.CompositeSequenceIdArg
        • ubic.gemma.web.services.rest.util.args.CompositeSequenceNameArg
      • ubic.gemma.web.services.rest.util.args.DatabaseEntryArg<T>
        • ubic.gemma.web.services.rest.util.args.DatabaseEntryIdArg
        • ubic.gemma.web.services.rest.util.args.DatabaseEntryStringArg
      • ubic.gemma.web.services.rest.util.args.DatasetArg<T>
        • ubic.gemma.web.services.rest.util.args.DatasetIdArg
        • ubic.gemma.web.services.rest.util.args.DatasetStringArg
      • ubic.gemma.web.services.rest.util.args.ExpressionAnalysisResultSetArg
      • ubic.gemma.web.services.rest.util.args.FactorValueArg<A>
        • ubic.gemma.web.services.rest.util.args.FactorValueIdArg
        • ubic.gemma.web.services.rest.util.args.FactorValueValueArg
      • ubic.gemma.web.services.rest.util.args.GeneArg<T>
        • ubic.gemma.web.services.rest.util.args.GeneAnyIdArg<T>
          • ubic.gemma.web.services.rest.util.args.GeneEnsemblIdArg
          • ubic.gemma.web.services.rest.util.args.GeneNcbiIdArg
        • ubic.gemma.web.services.rest.util.args.GeneSymbolArg
      • ubic.gemma.web.services.rest.util.args.PlatformArg<T>
        • ubic.gemma.web.services.rest.util.args.PlatformIdArg
        • ubic.gemma.web.services.rest.util.args.PlatformStringArg
      • ubic.gemma.web.services.rest.util.args.QuantitationTypeArg<T>
        • ubic.gemma.web.services.rest.util.args.QuantitationTypeByIdArg
        • ubic.gemma.web.services.rest.util.args.QuantitationTypeByNameArg
      • ubic.gemma.web.services.rest.util.args.TaxonArg<T>
        • ubic.gemma.web.services.rest.util.args.TaxonIdArg
        • ubic.gemma.web.services.rest.util.args.TaxonNameArg
        • ubic.gemma.web.services.rest.util.args.TaxonNcbiIdArg
    • ubic.gemma.web.services.rest.util.args.BoolArg
    • ubic.gemma.web.services.rest.util.args.DoubleArg
    • ubic.gemma.web.services.rest.util.args.ExpLevelConsolidationArg
    • ubic.gemma.web.services.rest.util.args.FilterArg
    • ubic.gemma.web.services.rest.util.args.IntArg
    • ubic.gemma.web.services.rest.util.args.LimitArg
    • ubic.gemma.web.services.rest.util.args.LongArg
    • ubic.gemma.web.services.rest.util.args.OffsetArg
    • ubic.gemma.web.services.rest.util.args.SortArg
    • ubic.gemma.web.services.rest.util.args.StringArg
  • ubic.gemma.core.util.AbstractCLI (implements ubic.gemma.core.util.CLI)
    • ubic.gemma.core.util.AbstractSpringAwareCLI
      • ubic.gemma.core.util.AbstractCLIContextCLI
        • 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.CountObsoleteTermsCli
        • 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.MakeExperimentsPublicCli
          • ubic.gemma.core.apps.OrderVectorsByDesignCli
          • ubic.gemma.core.apps.ProcessedDataComputeCLI
          • 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.TwoChannelMissingValueCLI
          • 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.ExternalFileGeneLoaderCLI
        • ubic.gemma.core.apps.GenericGenelistDesignGenerator
        • ubic.gemma.core.apps.GeoGrabberCli
        • ubic.gemma.core.apps.IndexGemmaCLI
        • 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.UpdatePubMedCli
      • ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
    • 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>)
  • ubic.gemma.persistence.service.AbstractDao<T> (implements ubic.gemma.persistence.service.BaseDao<T>)
    • 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>)
        • 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>
          • ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<C,VO> (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>)
            • 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.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.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.common.description.BibliographicReferenceDaoImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceDao)
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao)
      • 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.expression.experiment.BlacklistedEntityDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityDao)
      • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao)
      • ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicDao)
      • 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.analysis.AnalysisDaoBase<T> (implements ubic.gemma.persistence.service.analysis.AnalysisDao<T>)
      • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao)
    • 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.common.auditAndSecurity.CurationDetailsDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsDao)
    • ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDaoImpl<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.RawExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao)
    • 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.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.web.services.rest.providers.AbstractExceptionMapper<E> (implements javax.ws.rs.ext.ExceptionMapper<E>)
    • ubic.gemma.web.services.rest.providers.AccessDeniedExceptionMapper
    • ubic.gemma.web.services.rest.providers.AuthenticationExceptionMapper
    • ubic.gemma.web.services.rest.providers.EntityNotFoundExceptionMapper
    • ubic.gemma.web.services.rest.providers.MalformedArgExceptionMapper
    • ubic.gemma.web.services.rest.providers.NotFoundExceptionMapper
    • ubic.gemma.web.services.rest.providers.UnhandledExceptionMapper
    • ubic.gemma.web.services.rest.providers.WebApplicationExceptionMapper
  • ubic.gemma.core.loader.util.fetcher.AbstractFetcher (implements ubic.gemma.core.loader.util.fetcher.Fetcher)
    • ubic.gemma.core.loader.util.fetcher.FtpFetcher
      • ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher (implements ubic.gemma.core.loader.util.fetcher.ArchiveFetcher)
        • ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
        • ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
        • ubic.gemma.core.loader.genome.taxon.TaxonFetcher
      • ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
          • ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
          • ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
      • ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
      • ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
    • ubic.gemma.core.loader.util.fetcher.HttpFetcher
  • ubic.gemma.core.loader.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
  • 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
  • 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.web.services.rest.swagger.resolvers.ArgModelResolver (implements ubic.gemma.web.services.rest.swagger.CustomModelConverter)
      • ubic.gemma.web.services.rest.swagger.resolvers.SearchResultTypeAllowableValuesModelResolver (implements ubic.gemma.web.services.rest.swagger.CustomModelConverter)
  • ubic.basecode.ontology.providers.AbstractOntologyService
    • ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService
      • ubic.gemma.core.ontology.providers.GemmaOntologyService
  • 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.RawExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService)
    • ubic.gemma.persistence.service.AbstractVoEnabledService<O,VO> (implements ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<O,VO> (implements 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.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.core.genome.gene.service.GeneServiceImpl (implements ubic.gemma.core.genome.gene.service.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.core.annotation.reference.BibliographicReferenceServiceImpl (implements ubic.gemma.core.annotation.reference.BibliographicReferenceService)
      • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService)
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayService)
      • 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.expression.experiment.BlacklistedEntityServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService)
      • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService)
      • ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicService)
      • 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.sequenceAnalysis.AnnotationAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService)
    • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService)
    • ubic.gemma.persistence.service.genome.ChromosomeServiceImpl (implements ubic.gemma.persistence.service.genome.ChromosomeService)
    • ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundService)
    • ubic.gemma.persistence.service.common.auditAndSecurity.ContactServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.ContactService)
    • 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.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.tasks.AbstractTask<T,C> (implements ubic.gemma.core.tasks.Task<T,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.core.analysis.service.AbstractTsvFileService<T> (implements ubic.gemma.core.analysis.service.TsvFileService<T>)
    • 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.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.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent.Factory
  • 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.AlternateNameImpl
  • 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
  • ubic.gemma.web.services.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.core.util.AnchorTagUtil
  • ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent.Factory
  • ubic.gemma.web.controller.expression.experiment.AnnotationController
  • ubic.gemma.web.services.rest.AnnotationsWebService
  • org.apache.log4j.AppenderSkeleton (implements org.apache.log4j.Appender, org.apache.log4j.spi.OptionHandler)
    • ubic.gemma.core.job.executor.common.ProgressUpdateAppender
    • ubic.gemma.web.logging.SlackAppender (implements org.apache.log4j.Appender)
  • ubic.gemma.web.services.rest.providers.ApplicationEventListener (implements org.glassfish.jersey.server.monitoring.ApplicationEventListener)
  • 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.GeneralSearchControllerImpl (implements ubic.gemma.web.controller.GeneralSearchController)
          • ubic.gemma.web.controller.genome.BlatResultTrackController
          • ubic.gemma.web.controller.common.auditAndSecurity.FileUploadController
  • ubic.gemma.web.services.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.ArrayDesignControllerImpl (implements ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController)
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent.Factory
  • ubic.gemma.web.taglib.arrayDesign.ArrayDesignHtmlUtil
  • ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl (implements ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService)
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent.Factory
  • 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.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent.Factory
  • 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.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent.Factory
  • ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService)
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent.Factory
  • ubic.gemma.persistence.util.ArrayDesignsForExperimentCache
  • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent.Factory
  • ubic.gemma.core.analysis.report.AuditableObject (implements java.io.Serializable)
  • ubic.gemma.core.security.audit.AuditableUtilImpl (implements ubic.gemma.core.security.audit.AuditableUtil)
  • ubic.gemma.model.common.auditAndSecurity.AuditAction (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.auditAndSecurity.AuditActionEnum (implements org.hibernate.usertype.EnhancedUserType)
  • 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.FailedDifferentialExpressionAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent
        • 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.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.BatchInformationFetchingEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent
          • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent
          • 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.BatchProblemsUpdateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
      • ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent
      • 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.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.SampleRemovalEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent
    • 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.LastUpdatedDateChangedEvent
      • 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.AuditTrailImpl
  • ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent.Factory
  • gemma.gsec.acl.BaseAclAdvice (implements org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.core.security.authorization.acl.AclAdvice
  • ubic.gemma.web.controller.BaseController
    • ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceControllerImpl (implements ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController)
    • ubic.gemma.web.controller.expression.designElement.CompositeSequenceController
    • ubic.gemma.web.controller.expression.experiment.ExperimentalDesignControllerImpl (implements 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.PubMedQueryControllerImpl (implements ubic.gemma.web.controller.common.description.bibref.PubMedQueryController)
    • ubic.gemma.web.controller.common.auditAndSecurity.SignupController
    • ubic.gemma.web.controller.common.auditAndSecurity.UserFormMultiActionController
  • 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.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.BaseValueObject (implements java.io.Serializable)
  • ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
    • ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
    • ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
    • ubic.gemma.core.loader.util.parser.LineMapParser<K,T>
      • ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
    • ubic.gemma.core.loader.genome.ProbeSequenceParser
    • ubic.gemma.core.loader.genome.taxon.TaxonParser
  • ubic.gemma.core.loader.util.parser.BasicLineParser<T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
    • ubic.gemma.core.loader.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
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundValueObject
  • ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent.Factory
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
  • 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)
  • ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent.Factory
  • ubic.gemma.core.util.BeanInitializationTimeMonitor (implements org.springframework.context.ApplicationListener<E>, org.springframework.beans.factory.config.BeanPostProcessor, org.springframework.core.Ordered)
  • ubic.gemma.persistence.util.BeanNameGenerator (implements org.springframework.beans.factory.support.BeanNameGenerator)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject (implements java.lang.Comparable<T>)
  • ubic.gemma.model.common.description.BibliographicReference.Factory
  • ubic.gemma.model.common.description.BibRefAnnotation (implements java.io.Serializable)
    • ubic.gemma.model.common.description.BibRefAnnotationImpl
      • 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.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.common.auditAndSecurity.eventType.BioMaterialMappingUpdate.Factory
  • 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.association.ReferenceAssociationImpl
  • 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.util.BusinessKey
  • ubic.gemma.web.util.CacheMonitorImpl (implements ubic.gemma.web.util.CacheMonitor)
  • ubic.gemma.persistence.util.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.CharacteristicByValueUriOrValueCount
  • 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.util.ChromosomeUtil
  • ubic.gemma.model.common.description.CitationValueObject (implements java.lang.Comparable<T>)
  • 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.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService)
  • 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
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand
  • 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
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject (implements java.lang.Comparable<T>)
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt (implements java.lang.Comparable<T>)
  • ubic.gemma.core.analysis.preprocess.batcheffects.ComBat<R,C>
  • ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent.Factory
  • 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.core.search.source.CompassSearchSource (implements ubic.gemma.core.search.SearchSource)
  • ubic.gemma.persistence.util.CompassUtils
  • 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>)
  • ubic.gemma.model.expression.biomaterial.Compound.Factory
  • 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.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
  • 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.model.common.auditAndSecurity.curation.CurationDetails (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent.Factory
  • ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsService)
  • ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent.Factory
  • ubic.gemma.web.services.rest.swagger.CustomModelConvertersRegistrationListener (implements javax.servlet.ServletContextListener)
  • ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent.Factory
  • 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 ubic.gemma.core.search.SearchSource)
  • ubic.gemma.core.search.source.DatabaseSearchSourceUtils
  • ubic.gemma.model.common.description.DatabaseType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.description.DatabaseTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl (implements ubic.gemma.core.analysis.report.DatabaseViewGenerator)
  • ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent.Factory
  • ubic.gemma.core.loader.expression.geo.DatasetCombiner
  • ubic.gemma.web.services.rest.DatasetsWebService
  • 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.model.common.Describable (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.common.AbstractAuditable (implements ubic.gemma.model.common.Auditable)
      • ubic.gemma.model.expression.arrayDesign.ArrayDesign (implements ubic.gemma.model.common.auditAndSecurity.curation.Curatable, gemma.gsec.model.SecuredNotChild)
      • ubic.gemma.model.analysis.expression.ExpressionExperimentSet (implements gemma.gsec.model.Securable)
      • ubic.gemma.model.genome.gene.GeneSet (implements gemma.gsec.model.SecuredNotChild)
      • ubic.gemma.model.analysis.Investigation (implements gemma.gsec.model.Securable)
        • ubic.gemma.model.expression.experiment.BioAssaySet
          • ubic.gemma.model.expression.experiment.ExpressionExperiment (implements ubic.gemma.model.common.auditAndSecurity.curation.Curatable, gemma.gsec.model.SecuredNotChild)
          • ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet (implements gemma.gsec.model.SecuredChild)
        • ubic.gemma.model.association.phenotype.GenericExperiment
      • ubic.gemma.model.association.phenotype.PhenotypeAssociation (implements gemma.gsec.model.Securable)
        • ubic.gemma.model.association.phenotype.DataAnalysisEvidence
          • ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence
            • ubic.gemma.model.association.phenotype.DifferentialExpressionEvidenceImpl
        • 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
      • ubic.gemma.model.analysis.expression.ExpressionAnalysis
        • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis (implements gemma.gsec.model.Securable)
        • ubic.gemma.model.analysis.SingleExperimentAnalysis (implements gemma.gsec.model.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
    • ubic.gemma.model.expression.bioAssay.BioAssay (implements gemma.gsec.model.SecuredChild)
    • ubic.gemma.model.expression.bioAssayData.BioAssayDimension
    • ubic.gemma.model.expression.biomaterial.BioMaterial (implements gemma.gsec.model.SecuredChild)
    • ubic.gemma.model.genome.biosequence.BioSequence
    • ubic.gemma.model.expression.BlacklistedEntity
      • ubic.gemma.model.expression.experiment.BlacklistedExperiment
      • ubic.gemma.model.expression.arrayDesign.BlacklistedPlatform
    • ubic.gemma.model.common.description.Characteristic
    • ubic.gemma.model.genome.ChromosomeFeature
      • ubic.gemma.model.genome.Gene
      • ubic.gemma.model.genome.gene.GeneProduct
    • ubic.gemma.model.expression.designElement.CompositeSequence
    • ubic.gemma.model.expression.biomaterial.Compound
    • ubic.gemma.model.common.auditAndSecurity.Contact (implements gemma.gsec.model.Contact)
      • ubic.gemma.model.common.auditAndSecurity.Person (implements gemma.gsec.model.Person)
        • ubic.gemma.model.common.auditAndSecurity.User (implements gemma.gsec.model.User)
    • ubic.gemma.model.expression.experiment.ExperimentalDesign (implements gemma.gsec.model.SecuredChild)
    • ubic.gemma.model.expression.experiment.ExperimentalFactor (implements gemma.gsec.model.SecuredChild)
    • ubic.gemma.model.common.description.ExternalDatabase (implements ubic.gemma.model.common.Auditable, ubic.gemma.model.common.description.Versioned)
    • ubic.gemma.model.common.protocol.Protocol (implements gemma.gsec.model.Securable)
    • ubic.gemma.model.common.quantitationtype.QuantitationType
      • ubic.gemma.model.common.quantitationtype.QuantitationTypeImpl
    • ubic.gemma.core.loader.expression.arrayDesign.Reporter
    • ubic.gemma.model.expression.biomaterial.Treatment
  • 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
  • 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.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent.Factory
  • 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
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService)
  • 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
  • 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
  • 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
  • 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)
  • ubic.gemma.model.analysis.expression.diff.Direction (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.analysis.expression.diff.DirectionEnum (implements org.hibernate.usertype.EnhancedUserType)
  • 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
  • ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent.Factory
  • ubic.gemma.core.util.DummyMailSender (implements org.springframework.mail.MailSender)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject
  • net.sf.ehcache.hibernate.EhCacheRegionFactory
    • ubic.gemma.persistence.util.ExternalCacheRegionFactory (implements org.springframework.context.ApplicationContextAware, org.springframework.beans.factory.InitializingBean)
  • 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.EmailNotificationContext
  • ubic.gemma.web.controller.EmptyController
  • ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject (implements java.io.Serializable)
  • ubic.gemma.web.remote.EntityDelegator
  • ubic.gemma.persistence.util.EntityUtils
  • 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
  • ubic.gemma.web.services.rest.util.ExceptionMapperUtils
  • ubic.gemma.core.job.executor.common.ExecutingTask<T> (implements java.util.concurrent.Callable<V>)
  • 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.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent.Factory
  • ubic.gemma.core.analysis.util.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
  • ubic.gemma.core.loader.expression.ExperimentPlatformSwitchHelperServiceImpl (implements ubic.gemma.core.loader.expression.ExperimentPlatformSwitchHelperService)
  • 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.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.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent.Factory
  • ubic.gemma.persistence.service.ExpressionExperimentPrePersistServiceImpl (implements ubic.gemma.persistence.service.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.core.expression.experiment.service.ExpressionExperimentSearchServiceImpl (implements ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService)
  • ubic.gemma.model.analysis.expression.ExpressionExperimentSet.Factory
  • ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl (implements ubic.gemma.core.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.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent.Factory
  • 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>)
  • 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.FactorType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.expression.experiment.FactorTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.model.expression.experiment.FactorValue (implements ubic.gemma.model.common.Identifiable, gemma.gsec.model.SecuredChild, java.io.Serializable)
  • ubic.gemma.model.expression.experiment.FactorValue.Factory
  • ubic.gemma.persistence.util.FactorValueComparator (implements java.util.Comparator<T>)
  • ubic.gemma.core.expression.experiment.FactorValueDeletionImpl (implements ubic.gemma.core.expression.experiment.FactorValueDeletion)
  • ubic.gemma.persistence.util.FactorValueVector
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent.Factory
  • 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.web.services.rest.util.args.FilterArg.Filter
  • ubic.gemma.core.analysis.preprocess.filter.FilterConfig (implements java.io.Serializable)
  • ubic.gemma.persistence.util.Filters (implements java.lang.Iterable<T>)
  • ubic.gemma.persistence.util.FiltersUtils
  • ubic.gemma.model.expression.experiment.Geeq (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent.Factory
  • ubic.gemma.web.controller.common.GemmaClassicHomePageController
  • ubic.gemma.core.apps.GemmaCLI
  • ubic.gemma.model.genome.Gene.Factory
  • ubic.gemma.persistence.model.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.Factory
  • ubic.gemma.model.association.Gene2OntologyEntryAssociation (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.association.Gene2OntologyEntryAssociationImpl
      • ubic.gemma.model.association.Gene2GOAssociation
  • 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
  • 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.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService)
  • 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.ontology.providers.GeneOntologyServiceImpl (implements ubic.gemma.core.ontology.providers.GeneOntologyService)
  • ubic.gemma.model.genome.GeneOntologyTermValueObject
  • ubic.gemma.web.controller.genome.gene.GenePickerController
  • ubic.gemma.model.genome.gene.GeneProduct.Factory
  • ubic.gemma.model.common.quantitationtype.GeneralType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.quantitationtype.GeneralTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • 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.web.services.rest.servlet.CorsFilter
      • ubic.gemma.web.services.rest.servlet.RestapidocsIndexRewriteFilter
  • ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl (implements ubic.gemma.core.genome.gene.service.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.core.genome.gene.service.GeneSetServiceImpl (implements ubic.gemma.core.genome.gene.service.GeneSetService)
  • ubic.gemma.core.genome.gene.GeneSetValueObjectHelperImpl (implements ubic.gemma.core.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.web.services.rest.GeneWebService
  • ubic.gemma.core.loader.expression.geo.service.GeoBrowser
  • ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl (implements ubic.gemma.core.loader.expression.geo.service.GeoBrowserService)
  • 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.model.association.GOEvidenceCode (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.association.GOEvidenceCodeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.core.externalDb.GoldenPath
    • ubic.gemma.core.externalDb.GoldenPathQuery
    • ubic.gemma.core.externalDb.GoldenPathSequenceAnalysis
  • ubic.gemma.core.ontology.GoMetric
  • 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.web.services.rest.providers.GzipWriterInterceptor (implements javax.ws.rs.ext.WriterInterceptor)
  • ubic.gemma.persistence.model.usertypes.HibernateByteBlobType (implements org.hibernate.usertype.UserType)
  • ubic.gemma.persistence.util.monitor.HibernateMonitorImpl (implements ubic.gemma.persistence.util.monitor.HibernateMonitor)
  • ubic.gemma.model.analysis.expression.diff.HitListSize (implements java.io.Serializable)
    • ubic.gemma.model.analysis.expression.diff.HitListSizeImpl
  • 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.model.IdentifiableValueObject<O> (implements ubic.gemma.model.common.Identifiable)
    • ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<C>
      • ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject (implements java.io.Serializable, ubic.gemma.model.common.description.Versioned)
        • ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignValueObjectExt
      • ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject (implements gemma.gsec.model.SecureValueObject)
        • ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
          • ubic.gemma.web.controller.expression.experiment.ExpressionExperimentEditValueObject
        • ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject
    • ubic.gemma.model.analysis.AnalysisResultSetValueObject<K,R>
      • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject
    • ubic.gemma.model.analysis.AnalysisResultValueObject<A>
      • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject
    • ubic.gemma.model.analysis.AnalysisValueObject<T>
      • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject (implements java.io.Serializable)
    • ubic.gemma.model.common.description.AnnotationValueObject
    • ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject (implements java.io.Serializable)
    • ubic.gemma.model.common.description.BibliographicReferenceValueObject
    • ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject (implements java.io.Serializable)
    • ubic.gemma.model.expression.bioAssay.BioAssayValueObject (implements java.io.Serializable)
    • ubic.gemma.model.expression.biomaterial.BioMaterialValueObject (implements java.io.Serializable)
    • ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
    • ubic.gemma.model.expression.BlacklistedValueObject (implements java.io.Serializable)
    • ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
    • ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicBasicValueObject
    • ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject (implements java.lang.Comparable<T>)
      • ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
    • ubic.gemma.model.expression.designElement.CompositeSequenceValueObject (implements java.io.Serializable)
    • ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
    • ubic.gemma.model.common.description.DatabaseEntryValueObject (implements java.io.Serializable)
      • ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
    • ubic.gemma.model.expression.bioAssayData.DataVectorValueObject (implements java.io.Serializable)
      • ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
      • ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
    • 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 (implements java.io.Serializable)
    • 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.GemmaSessionBackedValueObject)
        • ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
    • ubic.gemma.model.common.description.ExternalDatabaseValueObject (implements java.lang.Comparable<T>, java.io.Serializable, ubic.gemma.model.common.description.Versioned)
    • ubic.gemma.model.expression.experiment.FactorValueBasicValueObject (implements java.io.Serializable)
    • ubic.gemma.model.expression.experiment.FactorValueValueObject (implements java.io.Serializable)
    • ubic.gemma.model.expression.experiment.GeeqValueObject
      • ubic.gemma.model.expression.experiment.GeeqAdminValueObject
    • ubic.gemma.model.genome.gene.GeneProductValueObject (implements java.io.Serializable)
    • ubic.gemma.model.genome.gene.GeneSetValueObject (implements gemma.gsec.model.SecureValueObject)
      • ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject
      • ubic.gemma.core.genome.gene.SessionBoundGeneSetValueObject (implements ubic.gemma.model.GemmaSessionBackedValueObject)
        • ubic.gemma.core.genome.gene.FreeTextGeneResultsValueObject
        • ubic.gemma.core.genome.gene.GOGroupValueObject
        • ubic.gemma.core.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 (implements java.io.Serializable)
    • ubic.gemma.model.genome.TaxonValueObject (implements java.io.Serializable)
  • 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.indexer.IndexServiceImpl (implements ubic.gemma.core.search.indexer.IndexService)
  • ubic.gemma.web.services.rest.util.JacksonConfig
  • ubic.gemma.web.util.JavascriptLogger
  • ubic.gemma.model.common.auditAndSecurity.JobInfo (implements ubic.gemma.model.common.Identifiable, gemma.gsec.model.SecuredNotChild, java.io.Serializable)
  • ubic.gemma.model.common.auditAndSecurity.JobInfo.Factory
  • ubic.gemma.web.services.rest.providers.JsonMappingExceptionMapper (implements javax.ws.rs.ext.ExceptionMapper<E>)
  • ubic.gemma.web.remote.JsonReaderResponse<T>
  • ubic.gemma.web.view.JSONTableRenderer
  • ubic.gemma.web.view.JSONView (implements org.springframework.web.servlet.View)
  • ubic.gemma.model.common.description.Keyword.Factory
  • ubic.gemma.web.util.LabelValue (implements java.lang.Comparable<T>, java.io.Serializable)
  • 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.model.common.auditAndSecurity.eventType.LinkAnalysisEvent.Factory
  • 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.util.LinkUtils
  • 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.util.MailEngineImpl (implements ubic.gemma.persistence.util.MailEngine)
  • ubic.gemma.core.util.MailUtilsImpl (implements ubic.gemma.core.util.MailUtils)
  • ubic.gemma.web.controller.common.auditAndSecurity.MaintenanceModeController
  • ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent.Factory
  • ubic.gemma.core.datastructure.matrix.MatrixWriter
  • ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation (implements gemma.gsec.model.SecuredChild, java.io.Serializable)
  • ubic.gemma.model.expression.bioAssayData.MeanVarianceRelation.Factory
  • ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelperImpl (implements ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper)
  • 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.MeasurementImpl
  • ubic.gemma.model.common.measurement.Measurement.Factory
  • ubic.gemma.model.common.measurement.MeasurementKind (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.measurement.MeasurementKindEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.model.common.measurement.MeasurementType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.measurement.MeasurementTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.web.services.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.web.util.MinifierPostProcessor (implements net.jawr.web.resource.bundle.postprocess.ResourceBundlePostProcessor)
  • ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent.Factory
  • ubic.gemma.persistence.util.monitor.MonitorAdvice
  • 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.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.model.common.auditAndSecurity.eventType.NeedsAttentionEvent.Factory
  • 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.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent.Factory
  • ubic.gemma.persistence.util.ObjectAlias
  • ubic.gemma.persistence.util.ObjectFilter
  • ubic.gemma.persistence.util.ObjectFilterCriteriaUtils
  • ubic.gemma.persistence.util.ObjectFilterQueryUtils
  • ubic.gemma.web.services.rest.providers.ObjectMapperResolver (implements javax.ws.rs.ext.ContextResolver<T>)
  • ubic.gemma.web.controller.OntologyController
  • ubic.gemma.core.ontology.OntologyServiceImpl (implements ubic.gemma.core.ontology.OntologyService)
  • ubic.gemma.web.services.rest.util.OpenApiUtils
  • 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)
  • ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent.Factory
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • ubic.gemma.web.util.upload.MonitoredOutputStream
  • ubic.gemma.core.loader.util.ParserAndLoaderTools
  • ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent.Factory
  • 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.PhenotypeAssociationPublicationImpl
  • 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 org.springframework.beans.factory.InitializingBean, ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject (implements java.lang.Comparable<T>)
  • 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
  • ubic.gemma.web.services.rest.PhenotypeWebService
  • ubic.gemma.model.genome.PhysicalLocation.Factory
  • ubic.gemma.web.services.rest.PlatformsWebService
  • ubic.gemma.core.util.Pointcuts
  • ubic.gemma.model.genome.biosequence.PolymerType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.genome.biosequence.PolymerTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.web.controller.analysis.preprocess.PreprocessController
  • ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl (implements ubic.gemma.core.analysis.preprocess.PreprocessorService)
  • ubic.gemma.model.common.quantitationtype.PrimitiveType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.quantitationtype.PrimitiveTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • 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.persistence.service.expression.bioAssayData.ProcessedDataVectorCacheImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.persistence.service.expression.bioAssayData.ProcessedDataVectorCache)
  • ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector.Factory
  • ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperService)
  • ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent.Factory
  • 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.executor.common.ProgressUpdateAppender.ProgressUpdateContext (implements java.lang.AutoCloseable)
  • org.springframework.core.io.support.PropertiesLoaderSupport
    • org.springframework.beans.factory.config.PropertyResourceConfigurer (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor, org.springframework.core.PriorityOrdered)
      • org.springframework.beans.factory.config.PlaceholderConfigurerSupport (implements org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.BeanNameAware)
        • org.springframework.beans.factory.config.PropertyPlaceholderConfigurer
          • ubic.gemma.persistence.util.CommonsConfigurationPropertyPlaceholderConfigurer
  • 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.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
  • ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent.Factory
  • 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
  • ubic.gemma.core.loader.util.parser.RecordParser<T> (implements ubic.gemma.core.loader.util.parser.Parser<T>)
    • ubic.gemma.core.loader.genome.FastaParser
    • ubic.gemma.core.loader.genome.gene.SwissProtParser
  • ubic.gemma.model.association.ReferenceAssociation.Factory
  • ubic.gemma.persistence.util.ReflectionUtil
  • ubic.gemma.core.analysis.sequence.RepeatScan
  • ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
  • ubic.gemma.web.services.rest.providers.RequestExceptionLogger (implements org.glassfish.jersey.server.monitoring.RequestEventListener)
  • ubic.gemma.web.util.RequestUtil
  • ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent.Factory
  • ubic.gemma.web.services.rest.util.Responder
  • ubic.gemma.web.services.rest.util.ResponseDataObject<T>
    • ubic.gemma.web.services.rest.util.PaginatedResponseDataObject<T>
    • ubic.gemma.web.services.rest.SearchWebService.SearchResultsResponseDataObject
  • ubic.gemma.web.services.rest.util.ResponseErrorObject
  • ubic.gemma.web.services.rest.security.RestAuthEntryPoint (implements org.springframework.security.web.AuthenticationEntryPoint, org.springframework.web.context.ServletConfigAware)
  • org.springframework.retry.listener.RetryListenerSupport (implements org.springframework.retry.RetryListener)
    • ubic.gemma.persistence.retry.RetryLogger
  • ubic.gemma.web.services.rest.RootWebService
  • ubic.gemma.web.services.rest.RootWebService.ApiInfoValueObject
  • 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
  • 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.common.auditAndSecurity.eventType.SampleRemovalEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent.Factory
  • ubic.gemma.model.common.quantitationtype.ScaleType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.quantitationtype.ScaleTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.web.scheduler.SchedulerUtils
  • ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject
  • 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.model.common.search.SearchSettingsValueObject (implements java.io.Serializable)
  • ubic.gemma.web.services.rest.SearchWebService
  • ubic.gemma.web.services.rest.SearchWebService.SearchResultValueObject<T>
  • ubic.gemma.web.services.rest.SearchWebService.SearchSettingsValueObject
  • ubic.gemma.web.controller.common.auditAndSecurity.SecurityControllerImpl (implements ubic.gemma.web.controller.common.auditAndSecurity.SecurityController)
  • ubic.gemma.web.controller.common.auditAndSecurity.SecurityInfoValueObject
  • ubic.gemma.persistence.util.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.biosequence.SequenceType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.genome.biosequence.SequenceTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.core.analysis.sequence.SequenceWriter
  • 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.services.rest.util.ServletUtils
  • ubic.gemma.web.persistence.SessionListManagerImpl (implements ubic.gemma.web.persistence.SessionListManager)
  • ubic.gemma.persistence.util.Settings
  • ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
  • ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
  • ubic.gemma.core.apps.ShellDelegatingBlat (implements ubic.gemma.core.apps.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.web.controller.common.auditAndSecurity.recaptcha.SimpleHttp
  • ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject (implements java.lang.Comparable<T>)
  • ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent.Factory
  • ubic.gemma.persistence.util.Sort
  • ubic.gemma.web.services.rest.util.args.SortArg.Sort
  • ubic.gemma.web.services.rest.util.SortValueObject
  • ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl (implements ubic.gemma.core.analysis.preprocess.SplitExperimentService)
  • ubic.gemma.persistence.util.SpringContextUtil
  • ubic.gemma.model.common.quantitationtype.StandardQuantitationType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.common.quantitationtype.StandardQuantitationTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • ubic.gemma.core.util.StopWatchUtils
  • ubic.gemma.core.util.StopWatchUtils.StopWatchRegion (implements java.lang.AutoCloseable)
  • ubic.gemma.web.remote.StringPoint
  • ubic.gemma.web.services.rest.util.StringUtils
  • ubic.gemma.core.job.executor.webapp.SubmittedTaskAbstract<T> (implements ubic.gemma.core.job.SubmittedTask<T>)
    • ubic.gemma.core.job.executor.webapp.SubmittedTaskLocal<T>
  • ubic.gemma.core.job.executor.webapp.SubmittedTasksMaintenance
  • ubic.gemma.core.job.progress.SubmittedTaskValueObject (implements java.io.Serializable)
  • 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.TableMaintenanceUtilImpl (implements ubic.gemma.persistence.service.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.core.job.executor.common.TaskCommandToTaskMatcherImpl (implements ubic.gemma.core.job.executor.common.TaskCommandToTaskMatcher)
  • ubic.gemma.web.controller.TaskCompletionController
  • ubic.gemma.core.job.executor.common.TaskPostProcessingImpl (implements ubic.gemma.core.job.executor.common.TaskPostProcessing)
  • ubic.gemma.core.job.TaskResult (implements java.io.Serializable)
    • ubic.gemma.core.tasks.maintenance.IndexerResult
  • ubic.gemma.core.job.executor.webapp.TaskRunningServiceImpl (implements ubic.gemma.core.job.executor.webapp.TaskRunningService)
  • ubic.gemma.web.services.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.util.TaxonUtility
  • ubic.gemma.model.expression.arrayDesign.TechnologyType (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.expression.arrayDesign.TechnologyTypeEnum (implements org.hibernate.usertype.EnhancedUserType)
  • java.lang.Thread (implements java.lang.Runnable)
    • ubic.gemma.core.util.concurrent.GenericStreamConsumer
    • ubic.gemma.core.util.concurrent.ParsingStreamConsumer<T>
  • ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethodEnum (implements org.hibernate.usertype.EnhancedUserType)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • ubic.gemma.web.services.rest.util.args.FilterArgParseException
      • ubic.gemma.core.analysis.preprocess.PreprocessingException
        • ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
          • 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.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.service.NoProcessedExpressionDataVectorsException
          • ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException
      • java.lang.RuntimeException
        • ubic.gemma.core.loader.util.AlreadyExistsInSystemException
        • ubic.gemma.core.association.phenotype.EntityNotFoundException
        • ubic.gemma.web.util.EntityNotFoundException
        • ubic.gemma.core.loader.util.parser.FileFormatException
        • ubic.gemma.web.controller.common.auditAndSecurity.recaptcha.ReCaptchaException
        • ubic.gemma.persistence.util.TaskCancelledException
        • ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException
        • java.lang.UnsupportedOperationException
          • ubic.gemma.core.analysis.preprocess.UnknownLogScaleException
        • javax.ws.rs.WebApplicationException
          • javax.ws.rs.ClientErrorException
            • javax.ws.rs.BadRequestException
              • ubic.gemma.web.services.rest.util.MalformedArgException
      • ubic.gemma.core.search.SearchException
        • ubic.gemma.core.search.BaseCodeOntologySearchException
        • ubic.gemma.core.search.CompassSearchException
  • ubic.gemma.core.util.TimeUtil
  • ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent.Factory
  • 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.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent.Factory
  • ubic.gemma.web.controller.analysis.preprocess.TwoChannelMissingValueController
  • ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService)
  • ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl (implements ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues)
  • ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent.Factory
  • ubic.gemma.model.common.measurement.Unit (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.common.measurement.UnitImpl
  • ubic.gemma.model.common.measurement.Unit.Factory
  • ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent.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.UserListControllerImpl (implements 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 gemma.gsec.model.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
  • ubic.gemma.core.analysis.preprocess.VectorMergingHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.VectorMergingHelperService)
  • ubic.gemma.web.controller.visualization.VisualizationValueObject
  • ubic.gemma.web.controller.WebConstants
  • ubic.gemma.web.services.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.persistence.service.analysis.AnalysisService<T>
  • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService
  • ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
• ubic.gemma.core.analysis.expression.AnalysisUtilService
• ubic.gemma.web.services.rest.util.args.Arg<T>
• ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
• ubic.gemma.web.controller.expression.arrayDesign.ArrayDesignController
• 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.core.security.audit.AuditableUtil
• ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
• ubic.gemma.persistence.service.common.auditAndSecurity.AuditHelper
• 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.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.bioAssay.BioAssayDao
    • 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.expression.experiment.BlacklistedEntityDao
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
    • ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
    • 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.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
      • ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
      • 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.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>)
      • 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.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.BaseVoEnabledDao<O,VO>)
  • 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.common.auditAndSecurity.CurationDetailsDao
  • ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao<T>
    • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
    • 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.FilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
      • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
      • ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
      • 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.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C,VO>)
      • 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.genome.gene.GeneSetDao
  • 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.common.measurement.UnitDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
• ubic.gemma.persistence.service.BaseService<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.genome.sequenceAnalysis.AnnotationAssociationService
  • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
  • ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>
    • ubic.gemma.core.annotation.reference.BibliographicReferenceService
    • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService
    • ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.FilteringService<O>)
    • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService
    • ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
    • ubic.gemma.persistence.service.expression.experiment.BlacklistedEntityService
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService
    • ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.FilteringService<O>)
    • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService
    • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService
    • ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.FilteringService<O>)
      • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
      • ubic.gemma.persistence.service.common.description.DatabaseEntryService
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
      • ubic.gemma.persistence.service.expression.experiment.FactorValueService
      • ubic.gemma.core.genome.gene.service.GeneService
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
      • ubic.gemma.persistence.service.genome.taxon.TaxonService
    • ubic.gemma.persistence.service.expression.experiment.GeeqService
    • ubic.gemma.persistence.service.genome.gene.GeneProductService
  • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
  • ubic.gemma.persistence.service.genome.ChromosomeService
  • ubic.gemma.persistence.service.expression.biomaterial.CompoundService
  • ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
  • ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorService<T>
    • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
    • ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
  • ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
  • ubic.gemma.persistence.service.common.description.ExternalDatabaseService
  • ubic.gemma.persistence.service.FilteringService<O>
    • ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (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.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService
      • ubic.gemma.persistence.service.common.description.DatabaseEntryService
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
      • ubic.gemma.persistence.service.expression.experiment.FactorValueService
      • ubic.gemma.core.genome.gene.service.GeneService
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService
      • ubic.gemma.persistence.service.genome.taxon.TaxonService
  • 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.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
• ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService
• ubic.gemma.web.controller.common.description.bibref.BibliographicReferenceController
• ubic.gemma.core.apps.Blat
• ubic.gemma.web.util.CacheMonitor
• java.util.concurrent.Callable<V>
  • ubic.gemma.core.tasks.Task<T,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.persistence.service.association.coexpression.CoexpressionCache
• ubic.gemma.persistence.service.association.coexpression.CoexpressionDao
• ubic.gemma.persistence.service.association.coexpression.CoexpressionService
• ubic.gemma.core.loader.util.converter.Converter<S,T>
  • ubic.gemma.core.loader.expression.geo.GeoConverter
• ubic.gemma.persistence.service.common.auditAndSecurity.CurationDetailsService
• ubic.gemma.core.analysis.report.DatabaseViewGenerator
• 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.core.job.executor.common.ExecutingTask.TaskLifecycleHandler
• ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController
• 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.persistence.service.ExpressionExperimentPrePersistService
• ubic.gemma.core.analysis.report.ExpressionExperimentReportService
• ubic.gemma.core.expression.experiment.service.ExpressionExperimentSearchService
• ubic.gemma.core.expression.experiment.ExpressionExperimentSetValueObjectHelper
• ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
• ubic.gemma.core.expression.experiment.FactorValueDeletion
• 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.model.GemmaSessionBackedValueObject
• ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService
• ubic.gemma.core.genome.gene.service.GeneCoreService
• ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
• ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService
• ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService
• ubic.gemma.web.controller.GeneralSearchController
• ubic.gemma.core.genome.gene.service.GeneSearchService
• ubic.gemma.core.search.GeneSetSearch
• ubic.gemma.core.genome.gene.service.GeneSetService
• ubic.gemma.core.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
• org.springframework.security.provisioning.GroupManager
  • gemma.gsec.authentication.UserManager (also extends org.springframework.security.provisioning.UserDetailsManager)
    • ubic.gemma.core.security.authentication.UserManager
• ubic.gemma.persistence.util.monitor.HibernateMonitor
• ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
• ubic.gemma.model.common.Identifiable
  • ubic.gemma.model.common.Auditable
    • ubic.gemma.model.common.auditAndSecurity.curation.Curatable
• ubic.gemma.core.search.indexer.IndexService
• org.springframework.beans.factory.InitializingBean
  • ubic.gemma.core.ontology.providers.GeneOntologyService
  • ubic.gemma.core.ontology.OntologyService
• ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister
• ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService
• ubic.gemma.persistence.util.MailEngine
• ubic.gemma.core.util.MailUtils
• java.util.Map<K,V>
  • org.springframework.util.MultiValueMap<K,V>
    • ubic.gemma.core.search.SearchService.SearchResultMap
• 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.swagger.v3.core.converter.ModelConverter
  • ubic.gemma.web.services.rest.swagger.CustomModelConverter
• 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>
• 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.persistence.service.expression.bioAssayData.ProcessedDataVectorCache
• ubic.gemma.core.analysis.preprocess.ProcessedExpressionDataVectorCreateHelperService
• ubic.gemma.web.job.progress.ProgressStatusService
• ubic.gemma.core.job.executor.common.ProgressUpdateAppender.ProgressUpdateCallback
• ubic.gemma.web.controller.common.description.bibref.PubMedQueryController
• ubic.gemma.core.loader.util.QueuingParser<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.SearchSource
• ubic.gemma.web.controller.common.auditAndSecurity.SecurityController
• 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<T>
• ubic.gemma.core.analysis.preprocess.svd.SVDService
• ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
• ubic.gemma.persistence.service.TableMaintenanceUtil
• ubic.gemma.core.job.executor.common.TaskCommandToTaskMatcher
• ubic.gemma.core.job.executor.common.TaskPostProcessing
• ubic.gemma.core.job.executor.webapp.TaskRunningService
• ubic.gemma.core.analysis.service.TsvFileService<T>
  • ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService
  • ubic.gemma.core.analysis.service.ExpressionDataFileService
• 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.web.controller.common.auditAndSecurity.UserListController
• gemma.gsec.authentication.UserService
  • ubic.gemma.core.security.authentication.UserService
• ubic.gemma.core.analysis.preprocess.VectorMergingHelperService
• ubic.gemma.core.analysis.preprocess.VectorMergingService
• ubic.gemma.model.common.description.Versioned
• ubic.gemma.core.analysis.report.WhatsNewService

Annotation Type Hierarchy

• ubic.gemma.model.annotations.GemmaWebOnly (implements java.lang.annotation.Annotation)
• ubic.gemma.web.services.rest.annotations.GZIP (implements java.lang.annotation.Annotation)
• ubic.gemma.persistence.util.monitor.Monitored (implements java.lang.annotation.Annotation)
• ubic.gemma.persistence.retry.Retryable (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao.QueryHint
    • ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter.Pattern
    • ubic.gemma.core.analysis.service.ArrayDesignAnnotationService.OutputType
    • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl.AnalysisType
    • ubic.gemma.core.loader.entrez.EutilFetch.Mode
    • ubic.gemma.core.apps.GemmaCLI.CommandGroup
    • ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl.GOAspect
    • 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.core.ontology.GoMetric.Metric
    • ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.NormalizationMethod
    • ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig.SingularThreshold
    • ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.GeneType
    • ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo.NomenclatureStatus
    • ubic.gemma.persistence.util.ObjectFilter.Operator
    • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao.RankMethod
    • ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter.Method
    • ubic.gemma.core.apps.ShellDelegatingBlat.BlattableGenome
    • ubic.gemma.persistence.util.Sort.Direction
    • ubic.gemma.web.services.rest.util.args.SortArg.Sort.Direction
    • ubic.gemma.core.job.SubmittedTask.Status