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.association.phenotype,
• ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence,
• ubic.gemma.core.config,
• ubic.gemma.core.context,
• ubic.gemma.core.datastructure.matrix,
• ubic.gemma.core.goldenpath,
• ubic.gemma.core.image,
• ubic.gemma.core.image.aba,
• ubic.gemma.core.job,
• ubic.gemma.core.job.notification,
• 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.metrics,
• ubic.gemma.core.metrics.binder,
• ubic.gemma.core.metrics.binder.cache,
• ubic.gemma.core.metrics.binder.database,
• ubic.gemma.core.metrics.binder.jpa,
• ubic.gemma.core.ontology,
• ubic.gemma.core.ontology.jena,
• ubic.gemma.core.ontology.providers,
• ubic.gemma.core.profiling,
• ubic.gemma.core.search,
• ubic.gemma.core.search.lucene,
• ubic.gemma.core.search.source,
• ubic.gemma.core.security,
• 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.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.blacklist,
• 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.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,
• ubic.gemma.persistence.cache,
• ubic.gemma.persistence.hibernate,
• 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.auditAndSecurity.curation,
• ubic.gemma.persistence.service.blacklist,
• 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.service.maintenance,
• ubic.gemma.persistence.util

Class Hierarchy

• java.lang.Object
  • ubic.gemma.core.image.aba.AbaGene
  • ubic.gemma.core.image.ABALinkOutValueObject (implements java.io.Serializable)
  • org.springframework.security.acls.afterinvocation.AbstractAclProvider (implements org.springframework.security.access.AfterInvocationProvider)
    • org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
      • gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationCollectionFilteringProvider
        • gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationByAssociationCollectionFilteringProvider
          • ubic.gemma.core.security.authorization.acl.AclAfterCollectionCompSeqByArrayDesignFilter
          • ubic.gemma.core.security.authorization.acl.AclAfterCollectionDataVectorByExpressionExperimentFilter
    • org.springframework.security.acls.afterinvocation.AclEntryAfterInvocationProvider (implements org.springframework.context.MessageSourceAware)
      • gemma.gsec.acl.afterinvocation.AclEntryAfterInvocationByAssociationFilteringProvider
        • ubic.gemma.core.security.authorization.acl.AclAfterCompSeqByArrayDesignFilter
  • ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer
    • ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer (implements ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer)
      • ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer (implements org.springframework.beans.factory.DisposableBean)
  • ubic.gemma.core.context.AbstractAsyncFactoryBean<T> (implements ubic.gemma.core.context.AsyncFactoryBean<T>, org.springframework.beans.factory.DisposableBean)
    • ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceFactory
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • ubic.gemma.persistence.util.Slice<O> (implements java.util.List<E>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • ubic.gemma.core.search.SearchResultSet<T>
  • ubic.gemma.persistence.service.AbstractDao<T> (implements ubic.gemma.persistence.service.BaseDao<T>)
    • ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao<T> (implements ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao<T>)
      • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao)
      • ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDao)
      • ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao)
    • ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
      • ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>, org.springframework.beans.factory.InitializingBean)
        • ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao<O,VO>
          • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao)
          • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDaoImpl (implements ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao)
        • ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
          • ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<C,VO> (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
            • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl (implements ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao)
            • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao)
          • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl (implements ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao)
          • ubic.gemma.persistence.service.genome.GeneDaoImpl (implements ubic.gemma.persistence.service.genome.GeneDao, org.springframework.beans.factory.InitializingBean)
          • ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl (implements ubic.gemma.persistence.service.genome.taxon.TaxonDao)
      • ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao<O,VO> (implements ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
        • ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao)
        • ubic.gemma.persistence.service.common.description.CharacteristicDaoImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicDao)
        • ubic.gemma.persistence.service.common.description.DatabaseEntryDaoImpl (implements ubic.gemma.persistence.service.common.description.DatabaseEntryDao)
        • ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueDao)
      • ubic.gemma.persistence.service.common.description.BibliographicReferenceDaoImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceDao)
      • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDao)
      • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl (implements ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao)
      • ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl (implements ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao)
      • ubic.gemma.persistence.service.blacklist.BlacklistedEntityDaoImpl (implements ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao)
      • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao)
      • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao)
      • ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao)
      • ubic.gemma.persistence.service.expression.experiment.GeeqDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.GeeqDao)
      • ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneProductDao)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao)
    • ubic.gemma.persistence.service.genome.ChromosomeDaoImpl (implements ubic.gemma.persistence.service.genome.ChromosomeDao)
    • ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDaoImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDao)
    • ubic.gemma.persistence.service.expression.biomaterial.CompoundDaoImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.ContactDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.ContactDao)
    • ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDao)
    • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao)
    • ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao)
    • ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDao)
    • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao)
    • ubic.gemma.persistence.service.common.description.ExternalDatabaseDaoImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseDao)
    • ubic.gemma.persistence.service.association.Gene2GOAssociationDaoImpl (implements ubic.gemma.persistence.service.association.Gene2GOAssociationDao)
    • ubic.gemma.persistence.service.genome.gene.GeneAliasDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneAliasDao)
    • ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao)
    • ubic.gemma.persistence.service.association.phenotype.GenericEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.GenericEvidenceDao)
    • ubic.gemma.persistence.service.association.phenotype.GenericExperimentDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.GenericExperimentDao)
    • ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetDao)
    • ubic.gemma.persistence.service.genome.gene.GeneSetMemberDaoImpl (implements ubic.gemma.persistence.service.BaseDao<T>)
    • ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao)
    • ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl (implements ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao)
    • ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao)
    • ubic.gemma.persistence.service.common.protocol.ProtocolDaoImpl (implements ubic.gemma.persistence.service.common.protocol.ProtocolDao)
    • ubic.gemma.persistence.service.association.ReferenceAssociationDaoImpl (implements ubic.gemma.persistence.service.association.ReferenceAssociationDao)
    • ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDaoBase<T> (implements ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao<T>)
      • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDaoImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao)
    • ubic.gemma.persistence.service.expression.experiment.StatementDaoImpl (implements ubic.gemma.persistence.service.expression.experiment.StatementDao)
    • ubic.gemma.persistence.service.common.measurement.UnitDaoImpl (implements ubic.gemma.persistence.service.common.measurement.UnitDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.UserDao)
    • ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao)
  • ubic.gemma.model.common.AbstractDescribable (implements ubic.gemma.model.common.Describable)
    • ubic.gemma.model.common.auditAndSecurity.AbstractAuditable (implements ubic.gemma.model.common.auditAndSecurity.Auditable, java.io.Serializable)
      • ubic.gemma.model.expression.arrayDesign.ArrayDesign (implements ubic.gemma.model.common.auditAndSecurity.curation.Curatable, 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.ExperimentalEvidence
        • ubic.gemma.model.association.phenotype.GenericEvidence
        • ubic.gemma.model.association.phenotype.LiteratureEvidence
      • ubic.gemma.model.common.auditAndSecurity.UserGroup (implements gemma.gsec.model.UserGroup)
    • ubic.gemma.model.analysis.Analysis (implements java.io.Serializable)
      • ubic.gemma.model.analysis.expression.ExpressionAnalysis
        • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis (implements 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 (implements java.io.Serializable)
    • ubic.gemma.model.expression.bioAssay.BioAssay (implements gemma.gsec.model.SecuredChild, java.io.Serializable)
    • ubic.gemma.model.expression.bioAssayData.BioAssayDimension (implements java.io.Serializable)
    • ubic.gemma.model.expression.biomaterial.BioMaterial (implements gemma.gsec.model.SecuredChild, java.io.Serializable)
    • ubic.gemma.model.genome.biosequence.BioSequence (implements java.io.Serializable)
    • ubic.gemma.model.blacklist.BlacklistedEntity (implements java.io.Serializable)
      • ubic.gemma.model.blacklist.BlacklistedExperiment
      • ubic.gemma.model.blacklist.BlacklistedPlatform
    • ubic.gemma.model.common.description.Characteristic (implements java.lang.Comparable<T>, java.io.Serializable)
      • ubic.gemma.model.expression.experiment.Statement
    • ubic.gemma.model.genome.ChromosomeFeature (implements java.io.Serializable)
      • ubic.gemma.model.genome.Gene
      • ubic.gemma.model.genome.gene.GeneProduct
    • ubic.gemma.model.expression.designElement.CompositeSequence (implements java.io.Serializable)
    • ubic.gemma.model.expression.biomaterial.Compound (implements java.io.Serializable)
    • ubic.gemma.model.common.auditAndSecurity.Contact (implements java.io.Serializable)
      • ubic.gemma.model.common.auditAndSecurity.Person
        • ubic.gemma.model.common.auditAndSecurity.User (implements gemma.gsec.model.User)
    • ubic.gemma.model.expression.experiment.ExperimentalDesign (implements gemma.gsec.model.SecuredChild, java.io.Serializable)
    • ubic.gemma.model.expression.experiment.ExperimentalFactor (implements gemma.gsec.model.SecuredChild, java.io.Serializable)
    • ubic.gemma.model.common.description.ExternalDatabase (implements ubic.gemma.model.common.auditAndSecurity.Auditable, java.io.Serializable, ubic.gemma.model.common.description.Versioned)
    • ubic.gemma.model.common.protocol.Protocol (implements gemma.gsec.model.Securable, java.io.Serializable)
    • ubic.gemma.model.common.quantitationtype.QuantitationType (implements java.io.Serializable)
    • ubic.gemma.core.loader.expression.arrayDesign.Reporter (implements java.io.Serializable)
    • ubic.gemma.model.expression.biomaterial.Treatment (implements java.io.Serializable)
  • org.springframework.beans.factory.config.AbstractFactoryBean<T> (implements org.springframework.beans.factory.BeanClassLoaderAware, org.springframework.beans.factory.BeanFactoryAware, org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.FactoryBean<T>, org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.core.security.ManualAuthenticationServiceBasedSecurityContextFactory
    • ubic.gemma.core.ontology.providers.OntologyServiceFactory<T>
    • ubic.gemma.core.util.TextResourceToSetOfLinesFactoryBean
  • ubic.gemma.core.loader.util.fetcher.AbstractFetcher (implements ubic.gemma.core.loader.util.fetcher.Fetcher)
    • ubic.gemma.core.loader.util.fetcher.FtpFetcher
      • ubic.gemma.core.loader.util.fetcher.FtpArchiveFetcher (implements ubic.gemma.core.loader.util.fetcher.ArchiveFetcher)
        • ubic.gemma.core.loader.expression.arrayExpress.DataFileFetcher
        • ubic.gemma.core.loader.genome.gene.ncbi.NCBIGeneFileFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.RawDataFetcher
        • ubic.gemma.core.loader.genome.taxon.TaxonFetcher
      • ubic.gemma.core.loader.expression.geo.fetcher.GeoFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.DatasetFetcher
          • ubic.gemma.core.loader.expression.geo.fetcher.LocalDatasetFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.PlatformFetcher
        • ubic.gemma.core.loader.expression.geo.fetcher.SeriesFetcher
          • ubic.gemma.core.loader.expression.geo.fetcher.LocalSeriesFetcher
      • ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneFetcher
      • ubic.gemma.core.loader.expression.arrayExpress.SDRFFetcher
    • ubic.gemma.core.loader.util.fetcher.HttpFetcher
  • ubic.gemma.core.analysis.service.AbstractFileService<T> (implements ubic.gemma.core.analysis.service.JsonFileService<T>, ubic.gemma.core.analysis.service.TsvFileService<T>)
    • ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService)
    • ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl (implements ubic.gemma.core.analysis.service.ExpressionDataFileService)
    • ubic.gemma.core.datastructure.matrix.MatrixWriter
  • ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer
  • ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao.FilterablePropertyMeta
  • ubic.gemma.core.loader.expression.geo.service.AbstractGeoService (implements org.springframework.beans.factory.BeanFactoryAware, ubic.gemma.core.loader.expression.geo.service.GeoService)
    • ubic.gemma.core.loader.expression.geo.service.GeoServiceImpl
  • ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis (implements ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis)
    • ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics
      • ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics
  • ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.core.metrics.GenericMeterRegistryConfigurer
    • ubic.gemma.core.metrics.MeterRegistryEhcacheConfigurer
  • ubic.gemma.core.ontology.AbstractOntologyResourceSimple (implements ubic.basecode.ontology.model.OntologyResource, java.io.Serializable)
    • ubic.gemma.core.ontology.OntologyIndividualSimple (implements ubic.basecode.ontology.model.OntologyIndividual)
    • ubic.gemma.core.ontology.OntologyPropertySimple (implements ubic.basecode.ontology.model.OntologyProperty)
  • ubic.basecode.ontology.jena.AbstractOntologyService (implements ubic.basecode.ontology.providers.OntologyService)
    • ubic.basecode.ontology.providers.AbstractOntologyService
      • ubic.gemma.core.ontology.providers.GemmaOntologyService
      • ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl (implements ubic.gemma.core.ontology.providers.GeneOntologyService, org.springframework.beans.factory.InitializingBean)
      • ubic.gemma.core.ontology.providers.MondoOntologyService
      • ubic.gemma.core.ontology.providers.PatoOntologyService
  • ubic.gemma.persistence.persister.AbstractPersister (implements ubic.gemma.persistence.persister.Persister)
    • ubic.gemma.persistence.persister.CommonPersister
      • ubic.gemma.persistence.persister.GenomePersister
        • ubic.gemma.persistence.persister.ArrayDesignPersister
          • ubic.gemma.persistence.persister.ExpressionPersister (implements ubic.gemma.persistence.persister.PersisterHelper)
            • ubic.gemma.persistence.persister.RelationshipPersister
              • ubic.gemma.persistence.persister.PersisterHelperImpl (implements ubic.gemma.persistence.persister.PersisterHelper)
  • ubic.gemma.persistence.persister.AbstractPersister.Caches
  • ubic.gemma.persistence.service.AbstractService<O> (implements ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService<T>
      • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService)
      • ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService)
      • ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService)
    • ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<O,VO> (implements ubic.gemma.persistence.service.BaseService<O>, ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl (implements ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService)
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssay.BioAssayService)
      • ubic.gemma.persistence.service.common.description.CharacteristicServiceImpl (implements ubic.gemma.persistence.service.common.description.CharacteristicService)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl (implements ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService)
      • ubic.gemma.persistence.service.common.description.DatabaseEntryServiceImpl (implements ubic.gemma.persistence.service.common.description.DatabaseEntryService)
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService)
      • ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueService)
      • ubic.gemma.persistence.service.genome.gene.GeneServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneService)
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeServiceImpl (implements ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService)
      • ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl (implements ubic.gemma.persistence.service.genome.taxon.TaxonService)
    • ubic.gemma.persistence.service.AbstractVoEnabledService<O,VO> (implements ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl (implements ubic.gemma.persistence.service.common.description.BibliographicReferenceService)
      • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionServiceImpl (implements ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService)
      • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService)
      • ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl (implements ubic.gemma.persistence.service.genome.biosequence.BioSequenceService)
      • ubic.gemma.persistence.service.blacklist.BlacklistedEntityServiceImpl (implements ubic.gemma.persistence.service.blacklist.BlacklistedEntityService)
      • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService)
      • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService)
      • ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.GeeqService)
      • ubic.gemma.persistence.service.genome.gene.GeneProductServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneProductService)
      • ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetService)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService)
    • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationServiceImpl (implements ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService)
    • ubic.gemma.persistence.service.genome.ChromosomeServiceImpl (implements ubic.gemma.persistence.service.genome.ChromosomeService)
    • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService)
    • ubic.gemma.persistence.service.expression.biomaterial.CompoundServiceImpl (implements ubic.gemma.persistence.service.expression.biomaterial.CompoundService)
    • ubic.gemma.persistence.service.common.auditAndSecurity.ContactServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.ContactService)
    • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService)
    • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService)
    • ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService)
    • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService)
    • ubic.gemma.persistence.service.common.description.ExternalDatabaseServiceImpl (implements ubic.gemma.persistence.service.common.description.ExternalDatabaseService)
    • ubic.gemma.persistence.service.association.Gene2GOAssociationServiceImpl (implements ubic.gemma.persistence.service.association.Gene2GOAssociationService, org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService)
    • ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationServiceImpl (implements ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService)
    • ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService)
    • ubic.gemma.persistence.service.common.protocol.ProtocolServiceImpl (implements ubic.gemma.persistence.service.common.protocol.ProtocolService)
  • ubic.gemma.core.job.AbstractTask<C> (implements ubic.gemma.core.job.Task<C>)
    • ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapperTaskImpl
    • ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTask)
    • ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTask)
    • ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTaskImpl (implements ubic.gemma.core.tasks.maintenance.CharacteristicUpdateTask)
    • ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskImpl (implements ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTask)
    • ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl (implements ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTask)
    • ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskImpl (implements ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTask)
    • ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTask)
    • ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskImpl (implements ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTask)
    • ubic.gemma.core.tasks.maintenance.IndexerTaskImpl (implements ubic.gemma.core.tasks.maintenance.IndexerTask)
    • ubic.gemma.core.tasks.analysis.coexp.LinkAnalysisTaskImpl
    • ubic.gemma.core.tasks.analysis.expression.PreprocessTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.PreprocessExperimentTask)
    • ubic.gemma.core.tasks.analysis.expression.SvdTaskImpl (implements ubic.gemma.core.tasks.analysis.expression.SvdTask)
    • ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskImpl
  • ubic.gemma.persistence.util.AclCriteriaUtils
  • ubic.gemma.persistence.util.AclQueryUtils
  • ubic.gemma.core.loader.expression.arrayDesign.AffyChipTypeExtractor
  • ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize
  • ubic.gemma.core.analysis.preprocess.filter.AffyProbeNameFilter
  • ubic.gemma.core.image.aba.AllenBrainAtlasServiceImpl (implements ubic.gemma.core.image.aba.AllenBrainAtlasService)
  • ubic.gemma.model.expression.arrayDesign.AlternateName (implements java.io.Serializable)
  • ubic.gemma.model.expression.arrayDesign.AlternateName.Factory
  • ubic.gemma.model.analysis.AnalysisResult (implements ubic.gemma.model.common.Identifiable)
    • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult (implements java.io.Serializable)
  • ubic.gemma.model.analysis.AnalysisResultSet<R> (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet<R>
      • ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet (implements gemma.gsec.model.SecuredChild)
  • 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.model.genome.sequenceAnalysis.AnnotationAssociation.Factory
  • org.apache.log4j.AppenderSkeleton (implements org.apache.log4j.Appender, org.apache.log4j.spi.OptionHandler)
    • ubic.gemma.core.job.progress.ProgressUpdateAppender
  • ubic.gemma.model.expression.arrayDesign.ArrayDesign.Factory
  • ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl (implements ubic.gemma.core.analysis.service.ArrayDesignAnnotationService)
  • ubic.gemma.core.analysis.sequence.ArrayDesignMapResultServiceImpl (implements ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService)
  • ubic.gemma.core.loader.expression.arrayDesign.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.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService)
  • ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl (implements ubic.gemma.core.analysis.report.ArrayDesignReportService)
  • ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService)
  • ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl (implements ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService)
  • ubic.gemma.persistence.persister.ArrayDesignsForExperimentCache
  • ubic.gemma.core.context.AsyncFactoryBeanUtils
  • ubic.gemma.core.analysis.report.AuditableObject (implements java.io.Serializable)
  • ubic.gemma.core.security.audit.AuditAdvice
  • ubic.gemma.model.common.auditAndSecurity.AuditEvent (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.auditAndSecurity.AuditEvent.Factory
  • ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventServiceImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService)
  • ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType (implements java.io.Serializable)
    • ubic.gemma.model.common.auditAndSecurity.eventType.AnalysisSuitabilityEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionSuitabilityEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.ResetSuitabilityForDifferentialExpressionAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.UnsuitableForDifferentialExpressionAnalysisEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ManualAnnotationEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignGeneMappingEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.AlignmentBasedGeneMappingEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.AnnotationBasedGeneMappingEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignMergeEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignProbeRenamingEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignRepeatAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceUpdateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSubsumeCheckEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.CommentedEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.CurationDetailsEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.CurationNoteUpdateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.DoesNotNeedAttentionEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.NeedsAttentionEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FactorValueNeedsAttentionEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedDifferentialExpressionAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedLinkAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedMeanVarianceUpdateEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedMissingValueAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedPCAAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedProcessedVectorComputationEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedSampleCorrelationAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.NotTroubledStatusFlagEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.TroubledStatusFlagEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.ExperimentalDesignUpdatedEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.BatchCorrectionEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationFetchingEvent
          • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationFetchingEvent
            • ubic.gemma.model.common.auditAndSecurity.eventType.SingletonBatchInvalidEvent
            • ubic.gemma.model.common.auditAndSecurity.eventType.UninformativeFASTQHeadersForBatchingEvent
          • ubic.gemma.model.common.auditAndSecurity.eventType.SingleBatchDeterminationEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.BatchInformationMissingEvent
          • ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.BatchProblemsUpdateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.BioMaterialMappingUpdate
      • ubic.gemma.model.common.auditAndSecurity.eventType.DataAddedEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.DataRemovedEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.DifferentialExpressionAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentPlatformSwitchEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentVectorMergeEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.LinkAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.TooSmallDatasetLinkAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.MeanVarianceUpdateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.MissingValueAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.OutlierAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.OutlierFoundAnalysisEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.OutliersNotFoundAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.PCAAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ProcessedVectorComputationEvent
        • ubic.gemma.model.common.auditAndSecurity.eventType.RankComputationEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.SampleCorrelationAnalysisEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.SampleRemovalReversionEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.ExpressionExperimentUpdateFromGEOEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.GeeqEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.PermissionChangeEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.MakePrivateEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.MakePublicEvent
    • ubic.gemma.model.common.auditAndSecurity.eventType.VersionedEvent
      • ubic.gemma.model.common.auditAndSecurity.eventType.ReleaseDetailsUpdateEvent
  • ubic.gemma.model.common.auditAndSecurity.AuditTrail (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.auditAndSecurity.AuditTrail.Factory
  • gemma.gsec.acl.BaseAclAdvice
    • ubic.gemma.core.security.authorization.acl.AclAdvice
  • ubic.gemma.core.config.BaseCodeConfigurer (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
  • org.apache.commons.configuration2.event.BaseEventSource (implements org.apache.commons.configuration2.event.EventSource)
    • org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
      • ubic.gemma.core.config.PropertySourcesConfiguration (implements org.apache.commons.configuration2.Configuration)
  • ubic.gemma.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
  • ubic.gemma.model.common.BaseValueObject (implements java.io.Serializable)
  • ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
    • ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader
    • ubic.gemma.core.loader.expression.arrayDesign.IlluminaProbeReader
    • ubic.gemma.core.loader.util.parser.LineMapParser<K,T>
      • ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneEnsemblFileParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneHistoryParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneInfoParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
    • ubic.gemma.core.loader.genome.ProbeSequenceParser
    • ubic.gemma.core.loader.genome.taxon.TaxonParser
  • ubic.gemma.core.loader.util.parser.BasicLineParser<T> (implements ubic.gemma.core.loader.util.parser.LineParser<T>)
    • ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
    • ubic.gemma.core.loader.genome.BlatResultParser
    • ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser
    • ubic.gemma.core.loader.genome.gene.ncbi.NcbiGene2AccessionParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
    • ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser (implements ubic.gemma.core.loader.util.QueuingParser<T>)
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfound (implements java.io.Serializable)
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchConfoundUtils
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails.BatchEffectStatistics
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoParser
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService)
  • ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl (implements ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService)
  • ubic.gemma.core.context.BeanFactoryUtils
  • ubic.gemma.core.profiling.BeanInitializationTimeMonitor (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
  • ubic.gemma.core.context.BeanNameGenerator (implements org.springframework.beans.factory.support.BeanNameGenerator)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.BibliographicPhenotypesValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.model.common.description.BibliographicReference.Factory
  • ubic.gemma.model.common.description.BibRefAnnotation (implements java.io.Serializable)
    • ubic.gemma.model.common.description.Keyword
    • ubic.gemma.model.common.description.MedicalSubjectHeading
  • ubic.gemma.model.expression.bioAssay.BioAssay.Factory
  • ubic.gemma.model.expression.bioAssayData.BioAssayDimension.Factory
  • ubic.gemma.persistence.service.expression.experiment.BioAssaySetServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.BioAssaySetService)
  • ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher
  • ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiObjectGenerator
  • ubic.gemma.model.expression.biomaterial.BioMaterial.Factory
  • ubic.gemma.model.genome.biosequence.BioSequence.Factory
  • ubic.gemma.model.association.BioSequence2GeneProduct (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation
    • ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation
    • ubic.gemma.model.association.ReferenceAssociation
  • ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation.Factory
  • ubic.gemma.core.analysis.sequence.BlatAssociationScorer
  • ubic.gemma.model.genome.sequenceAnalysis.BlatResult.Factory
  • ubic.gemma.core.analysis.sequence.BlatResult2Psl
  • ubic.gemma.core.util.BuildInfo (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.persistence.util.BusinessKey
  • io.micrometer.core.instrument.binder.cache.CacheMeterBinder<C> (implements io.micrometer.core.instrument.binder.MeterBinder)
    • ubic.gemma.core.metrics.binder.cache.EhCache24Metrics
  • ubic.gemma.persistence.cache.CacheUtils
  • ubic.gemma.persistence.util.ChannelUtils
  • ubic.gemma.model.common.description.Characteristic.Factory
  • ubic.gemma.persistence.service.common.description.CharacteristicDao.CharacteristicUsageFrequency
  • ubic.gemma.model.common.description.CharacteristicUtils
  • ubic.gemma.model.genome.Chromosome (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.genome.ChromosomeLocation (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.genome.PhysicalLocation
  • ubic.gemma.persistence.service.genome.ChromosomeUtils
  • ubic.gemma.model.common.description.CitationValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution
  • ubic.gemma.model.analysis.expression.coexpression.CoexpCorrelationDistribution.Factory
  • ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis.Factory
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionCache, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionCacheValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionDao)
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject (implements java.io.Serializable)
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionSearchCommand (implements java.io.Serializable)
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl (implements ubic.gemma.persistence.service.association.coexpression.CoexpressionService)
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionSummaryValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt (implements java.lang.Comparable<T>)
  • ubic.gemma.persistence.util.CommonQueries
  • ubic.gemma.core.search.source.CompositeSearchSource (implements ubic.gemma.core.search.SearchSource)
  • ubic.gemma.model.expression.designElement.CompositeSequence.Factory
  • ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperService
  • ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary
  • ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.model.expression.biomaterial.Compound.Factory
  • ubic.gemma.model.common.auditAndSecurity.Contact.Factory
  • ubic.gemma.model.analysis.expression.diff.ContrastResult (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.ContrastResult.Factory
  • ubic.gemma.model.analysis.expression.diff.ContrastsValueObject (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.ContrastVO
  • ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.description.DatabaseEntry (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.description.DatabaseEntry.Factory
  • ubic.gemma.core.search.source.DatabaseSearchSource (implements org.springframework.core.Ordered, ubic.gemma.core.search.SearchSource)
  • ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl (implements ubic.gemma.core.analysis.report.DatabaseViewGenerator)
  • ubic.gemma.core.loader.expression.geo.DatasetCombiner
  • ubic.gemma.core.loader.expression.DataUpdaterImpl (implements ubic.gemma.core.loader.expression.DataUpdater)
  • ubic.gemma.model.expression.bioAssayData.DataVector (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.expression.bioAssayData.DesignElementDataVector
      • ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
      • ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector
  • ubic.gemma.core.search.DefaultHighlighter (implements ubic.gemma.core.search.lucene.LuceneHighlighter, ubic.gemma.core.search.OntologyHighlighter)
  • ubic.gemma.persistence.util.DescribableComparator (implements java.util.Comparator<T>)
  • org.hibernate.dialect.Dialect (implements org.hibernate.exception.spi.ConversionContext)
    • org.hibernate.dialect.H2Dialect
      • ubic.gemma.persistence.hibernate.H2Dialect
    • org.hibernate.dialect.MySQLDialect
      • org.hibernate.dialect.MySQL5Dialect
        • org.hibernate.dialect.MySQL5InnoDBDialect
          • org.hibernate.dialect.MySQL57InnoDBDialect
            • ubic.gemma.persistence.hibernate.MySQL57InnoDBDialect
  • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis.Factory
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig (implements java.io.Serializable)
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService)
  • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult.Factory
  • ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator (implements java.util.Comparator<T>)
  • ubic.gemma.persistence.util.DifferentialExpressionAnalysisResultComparator.Factory
  • ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject (implements java.io.Serializable)
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisUtil
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService)
  • ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence.Factory
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils
  • ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject (implements java.io.Serializable)
  • ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Cell
  • ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.Condition
  • ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject.DiffExGene
  • ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCacheImpl (implements ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject (implements java.io.Serializable)
  • ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerServiceImpl (implements ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService)
  • ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult (implements java.io.Serializable)
    • ubic.gemma.persistence.service.analysis.expression.diff.MissingResult
    • ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult
  • ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject (implements java.io.Serializable)
  • ubic.gemma.core.util.DummyMailSender (implements org.springframework.beans.factory.InitializingBean, org.springframework.mail.MailSender)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.DumpsValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.util.EE2CAclQueryUtils
  • ubic.gemma.persistence.cache.EhcacheConfig
  • ubic.gemma.persistence.cache.EhcacheKeyLock (implements ubic.gemma.persistence.cache.CacheKeyLock)
  • ubic.gemma.model.analysis.expression.pca.Eigenvalue (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.pca.Eigenvalue.Factory
  • ubic.gemma.model.analysis.expression.pca.Eigenvector (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.pca.Eigenvector.Factory
  • ubic.gemma.core.job.notification.EmailNotificationContext
  • ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.util.EntityUtils
  • org.hibernate.type.EnumType (implements org.hibernate.usertype.DynamicParameterizedType, org.hibernate.usertype.EnhancedUserType, org.hibernate.usertype.LoggableUserType, java.io.Serializable)
    • ubic.gemma.persistence.hibernate.BatchEffectType
  • ubic.gemma.core.context.EnvironmentProfiles
  • ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser
  • ubic.gemma.core.loader.entrez.EutilFetch
  • ubic.gemma.model.genome.gene.phenotype.EvidenceFilter
  • ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSecurityValueObject (implements java.io.Serializable)
  • ubic.gemma.model.expression.experiment.ExperimentalDesign.Factory
  • ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl (implements ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporter)
  • ubic.gemma.model.expression.experiment.ExperimentalDesignUtils
  • ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl (implements ubic.gemma.core.visualization.ExperimentalDesignVisualizationService)
  • ubic.gemma.core.datastructure.matrix.ExperimentalDesignWriter
  • ubic.gemma.model.association.phenotype.ExperimentalEvidence.Factory
  • ubic.gemma.model.expression.experiment.ExperimentalFactor.Factory
  • ubic.gemma.model.association.coexpression.ExperimentCoexpressionLink (implements java.io.Serializable)
    • ubic.gemma.model.association.coexpression.HumanExperimentCoexpressionLinkImpl
    • ubic.gemma.model.association.coexpression.MouseExperimentCoexpressionLinkImpl
    • ubic.gemma.model.association.coexpression.OtherExperimentCoexpressionLinkImpl
    • ubic.gemma.model.association.coexpression.RatExperimentCoexpressionLinkImpl
  • ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject (implements java.io.Serializable)
  • ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject (implements java.io.Serializable)
  • ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet.Factory
  • ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil
  • ubic.gemma.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.core.analysis.preprocess.filter.ExpressionExperimentFilter
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentPrePersistService)
  • ubic.gemma.core.analysis.report.ExpressionExperimentReportServiceImpl (implements ubic.gemma.core.analysis.report.ExpressionExperimentReportService, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService)
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
  • ubic.gemma.model.analysis.expression.ExpressionExperimentSet.Factory
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelperImpl (implements ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper)
  • ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.Factory
  • ubic.gemma.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.description.ExternalDatabase.Factory
  • ubic.gemma.model.common.description.ExternalDatabases
  • ubic.gemma.model.genome.gene.phenotype.valueObject.ExternalDatabaseStatisticsValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.core.loader.util.parser.ExternalDatabaseUtils
  • ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl (implements ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService)
  • ubic.gemma.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.persistence.service.expression.experiment.FactorValueDeletionImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion)
  • ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.Migration
  • ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationResult
  • ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl (implements ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService)
  • ubic.gemma.core.ontology.FactorValueOntologyService.OntologyStatement
  • ubic.gemma.core.ontology.FactorValueOntologyServiceImpl (implements ubic.gemma.core.ontology.FactorValueOntologyService)
  • ubic.gemma.core.ontology.FactorValueOntologyUtils
  • ubic.gemma.core.ontology.FactorValueOntologyUtils.Annotation
  • ubic.gemma.core.ontology.FactorValueOntologyUtils.AnnotationIds
  • ubic.gemma.model.expression.experiment.FactorValueUtils
  • ubic.gemma.persistence.util.FactorValueVector
  • ubic.gemma.persistence.util.Filter (implements ubic.gemma.persistence.util.PropertyMapping)
  • ubic.gemma.core.analysis.preprocess.filter.FilterConfig (implements java.io.Serializable)
  • ubic.gemma.persistence.util.FilterCriteriaUtils
  • ubic.gemma.persistence.util.FilterQueryUtils
  • ubic.gemma.persistence.util.Filters (implements java.lang.Iterable<T>)
  • ubic.gemma.persistence.util.Filters.FiltersClauseBuilder
  • ubic.gemma.persistence.util.FiltersUtils
  • ubic.gemma.model.expression.experiment.Geeq (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.core.util.GemmaRestApiClientImpl (implements ubic.gemma.core.util.GemmaRestApiClient)
  • ubic.gemma.model.genome.Gene.Factory
  • ubic.gemma.persistence.service.maintenance.Gene2CsStatus (implements java.io.Serializable)
  • ubic.gemma.model.association.Gene2GeneAssociation (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.association.Gene2GeneIdAssociation (implements java.io.Serializable)
    • ubic.gemma.model.association.coexpression.Gene2GeneCoexpression (implements java.lang.Comparable<T>)
      • ubic.gemma.model.association.coexpression.HumanGeneCoExpression
        • ubic.gemma.model.association.coexpression.HumanGeneCoExpressionImpl
      • ubic.gemma.model.association.coexpression.MouseGeneCoExpression
        • ubic.gemma.model.association.coexpression.MouseGeneCoExpressionImpl
      • ubic.gemma.model.association.coexpression.OtherGeneCoExpression
        • ubic.gemma.model.association.coexpression.OtherGeneCoExpressionImpl
      • ubic.gemma.model.association.coexpression.RatGeneCoExpression
        • ubic.gemma.model.association.coexpression.RatGeneCoExpressionImpl
  • ubic.gemma.model.association.Gene2GOAssociation.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 (implements java.io.Serializable)
  • ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl (implements ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService)
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysis.Factory
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult.Factory
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject (implements gemma.gsec.model.SecureValueObject)
  • ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl (implements ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService)
  • ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperServiceImpl (implements ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService)
  • ubic.gemma.core.analysis.sequence.GeneMappingSummary (implements java.io.Serializable)
  • ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationServiceImpl (implements ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService)
  • ubic.gemma.model.genome.GeneOntologyTermValueObject (implements java.io.Serializable)
  • ubic.gemma.model.genome.gene.GeneProduct.Factory
  • ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDaoImpl (implements ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDao)
  • ubic.gemma.model.association.phenotype.GenericEvidence.Factory
  • ubic.gemma.model.association.phenotype.GenericExperiment.Factory
  • ubic.gemma.persistence.service.genome.gene.GeneSearchServiceImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSearchService)
  • ubic.gemma.model.genome.gene.GeneSet.Factory
  • ubic.gemma.model.genome.gene.GeneSetMember (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.genome.gene.GeneSetMember.Factory
  • ubic.gemma.core.search.GeneSetSearchImpl (implements ubic.gemma.core.search.GeneSetSearch)
  • ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl (implements ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper)
  • ubic.gemma.persistence.service.association.coexpression.GeneTestedInCacheImpl (implements ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.core.loader.expression.geo.service.GeoBrowser
  • ubic.gemma.core.loader.expression.geo.service.GeoBrowserServiceImpl (implements org.springframework.beans.factory.DisposableBean, ubic.gemma.core.loader.expression.geo.service.GeoBrowserService, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.core.loader.expression.geo.model.GeoChannel
  • ubic.gemma.core.loader.expression.geo.util.GeoConstants
  • ubic.gemma.core.loader.expression.geo.model.GeoContact (implements java.io.Serializable)
  • ubic.gemma.core.loader.expression.geo.GeoConverterImpl (implements ubic.gemma.core.loader.expression.geo.GeoConverter)
  • ubic.gemma.core.loader.expression.geo.model.GeoData (implements java.io.Serializable)
    • ubic.gemma.core.loader.expression.geo.model.GeoDataset
    • ubic.gemma.core.loader.expression.geo.model.GeoPlatform
    • ubic.gemma.core.loader.expression.geo.model.GeoRecord
    • ubic.gemma.core.loader.expression.geo.model.GeoSample (implements java.lang.Comparable<T>)
    • ubic.gemma.core.loader.expression.geo.model.GeoSeries
    • ubic.gemma.core.loader.expression.geo.model.GeoSubset
  • ubic.gemma.core.loader.expression.geo.GeoDomainObjectGenerator (implements ubic.gemma.core.loader.util.sdo.SourceDomainObjectGenerator)
    • ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal
  • ubic.gemma.core.loader.expression.geo.GeoFamilyParser (implements ubic.gemma.core.loader.util.parser.Parser<T>)
  • ubic.gemma.core.loader.expression.geo.GeoParseResult
  • ubic.gemma.core.loader.expression.geo.model.GeoReplication
  • ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence (implements java.io.Serializable)
  • ubic.gemma.core.loader.expression.geo.model.GeoValues (implements java.io.Serializable)
  • ubic.gemma.core.loader.expression.geo.model.GeoVariable
  • ubic.gemma.core.goldenpath.GoldenPath
    • ubic.gemma.core.goldenpath.GoldenPathQuery
    • ubic.gemma.core.goldenpath.GoldenPathSequenceAnalysis
  • ubic.gemma.core.ontology.GoMetricImpl (implements 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.core.metrics.binder.jpa.Hibernate4Metrics (implements io.micrometer.core.instrument.binder.MeterBinder)
  • ubic.gemma.core.metrics.binder.jpa.Hibernate4QueryMetrics (implements java.lang.AutoCloseable, io.micrometer.core.instrument.binder.MeterBinder)
  • ubic.gemma.core.search.source.HibernateSearchSource (implements ubic.gemma.core.search.FieldAwareSearchSource, org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.persistence.hibernate.HibernateUtils
  • ubic.gemma.core.metrics.binder.database.HikariCPMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
  • ubic.gemma.model.analysis.expression.diff.HitListSize (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.diff.HitListSize.Factory
  • ubic.gemma.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.common.IdentifiableValueObject<O> (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<C>
      • ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject (implements ubic.gemma.model.common.description.Versioned)
      • ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject (implements gemma.gsec.model.SecureValueObject)
        • ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject
        • 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
    • ubic.gemma.model.common.description.BibliographicReferenceValueObject
    • ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject
    • ubic.gemma.model.expression.bioAssay.BioAssayValueObject
    • ubic.gemma.model.expression.biomaterial.BioMaterialValueObject
    • ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject
    • ubic.gemma.model.blacklist.BlacklistedValueObject
    • ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject
    • ubic.gemma.model.common.description.CharacteristicValueObject (implements java.lang.Comparable<T>)
      • ubic.gemma.model.genome.gene.phenotype.valueObject.TreeCharacteristicValueObject
    • ubic.gemma.model.expression.designElement.CompositeSequenceValueObject
    • ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject
    • ubic.gemma.model.common.description.DatabaseEntryValueObject
      • ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceSourceValueObject
    • ubic.gemma.model.expression.bioAssayData.DataVectorValueObject
      • ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject
      • ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject
        • ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject
    • ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject<E> (implements java.lang.Comparable<T>, java.io.Serializable)
      • ubic.gemma.model.genome.gene.phenotype.valueObject.DiffExpressionEvidenceValueObject
      • ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject
      • ubic.gemma.model.genome.gene.phenotype.valueObject.GenericEvidenceValueObject
      • ubic.gemma.model.genome.gene.phenotype.valueObject.LiteratureEvidenceValueObject
    • ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject
    • ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject (implements java.lang.Comparable<T>, gemma.gsec.model.SecureValueObject)
      • ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject (implements ubic.gemma.model.common.GemmaSessionBackedValueObject)
        • ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject
    • ubic.gemma.model.common.description.ExternalDatabaseValueObject (implements java.lang.Comparable<T>, ubic.gemma.model.common.description.Versioned)
    • ubic.gemma.model.expression.experiment.FactorValueBasicValueObject
    • ubic.gemma.model.expression.experiment.FactorValueValueObject
    • ubic.gemma.model.expression.experiment.GeeqValueObject
      • ubic.gemma.model.expression.experiment.GeeqAdminValueObject
    • ubic.gemma.model.genome.gene.GeneProductValueObject
    • ubic.gemma.model.genome.gene.GeneSetValueObject (implements gemma.gsec.model.SecureValueObject)
      • ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject
      • ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject (implements ubic.gemma.model.common.GemmaSessionBackedValueObject)
        • ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject
        • ubic.gemma.model.genome.gene.GOGroupValueObject
        • ubic.gemma.model.genome.gene.PhenotypeGroupValueObject
    • ubic.gemma.model.genome.gene.GeneValueObject (implements java.io.Serializable)
      • ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject
    • ubic.gemma.model.common.measurement.MeasurementValueObject
    • ubic.gemma.model.genome.PhysicalLocationValueObject
    • ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject
    • ubic.gemma.model.expression.experiment.StatementValueObject (implements java.lang.Comparable<T>)
    • ubic.gemma.model.genome.TaxonValueObject
  • ubic.gemma.core.image.aba.Image
  • ubic.gemma.core.image.aba.ImageSeries
  • ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject (implements java.io.Serializable)
  • ubic.gemma.core.search.IndexerServiceImpl (implements ubic.gemma.core.search.IndexerService)
  • 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.model.common.description.Keyword.Factory
  • ubic.gemma.core.context.LazyInitByDefaultPostProcessor (implements org.springframework.beans.factory.config.BeanFactoryPostProcessor)
  • ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
  • ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig (implements java.io.Serializable)
  • 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.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.core.search.lucene.LuceneQueryUtils
  • ubic.gemma.core.util.MailEngineImpl (implements ubic.gemma.core.util.MailEngine)
  • 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.MeanVarianceServiceImpl (implements ubic.gemma.core.analysis.preprocess.MeanVarianceService)
  • ubic.gemma.model.common.measurement.Measurement (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.measurement.Measurement.Factory
  • ubic.gemma.model.common.description.MedicalSubjectHeading.Factory
  • 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.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.persistence.service.association.coexpression.NonPersistentNonOrderedCoexpLink (implements java.lang.Comparable<T>)
  • ubic.gemma.core.search.source.OntologySearchSource (implements ubic.gemma.core.search.SearchSource)
  • ubic.gemma.core.ontology.OntologyServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.ontology.OntologyService)
  • ubic.gemma.core.ontology.OntologyUtils
  • ubic.gemma.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.core.loader.util.ParserAndLoaderTools
  • ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
  • ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService)
  • ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication (implements java.io.Serializable)
  • ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication.Factory
  • ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl (implements ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper)
  • ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl (implements ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.model.association.phenotype.PhenotypeMappingType (implements java.lang.Comparable<T>, org.hibernate.usertype.EnhancedUserType, java.io.Serializable)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeValueObject (implements java.io.Serializable)
  • ubic.gemma.model.genome.PhysicalLocation.Factory
  • ubic.gemma.persistence.util.Pointcuts
  • ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.PreparedCoexMatrices
  • ubic.gemma.core.analysis.preprocess.PreprocessorServiceImpl (implements ubic.gemma.core.analysis.preprocess.PreprocessorService)
  • ubic.gemma.model.analysis.expression.pca.PrincipalComponentAnalysis.Factory
  • ubic.gemma.model.analysis.expression.pca.ProbeLoading (implements java.io.Serializable)
  • ubic.gemma.model.analysis.expression.pca.ProbeLoading.Factory
  • ubic.gemma.core.analysis.sequence.ProbeMapperConfig
  • ubic.gemma.core.analysis.sequence.ProbeMapperImpl (implements ubic.gemma.core.analysis.sequence.ProbeMapper)
  • ubic.gemma.core.analysis.sequence.ProbeMapUtils
  • ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector.Factory
  • ubic.gemma.core.profiling.ProfilingConfig
  • ubic.gemma.core.job.progress.ProgressData (implements java.io.Serializable)
  • ubic.gemma.core.job.progress.ProgressUpdateAppender.ProgressUpdateContext (implements java.lang.AutoCloseable)
  • ubic.gemma.persistence.util.PropertyMappingUtils
  • ubic.gemma.model.common.protocol.Protocol.Factory
  • ubic.gemma.core.loader.entrez.pubmed.PubMedSearch
  • 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.persistence.util.QueryUtils
  • ubic.gemma.model.association.coexpression.RatGeneCoExpression.Factory
  • ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector.Factory
  • ubic.gemma.core.loader.util.parser.RecordParser<T> (implements ubic.gemma.core.loader.util.parser.Parser<T>)
    • ubic.gemma.core.loader.genome.FastaParser
    • ubic.gemma.core.loader.genome.gene.SwissProtParser
  • ubic.gemma.model.association.ReferenceAssociation.Factory
  • ubic.gemma.core.analysis.sequence.RepeatScan
  • ubic.gemma.core.loader.expression.arrayDesign.Reporter.Factory
  • org.springframework.retry.listener.RetryListenerSupport (implements org.springframework.retry.RetryListener)
    • ubic.gemma.persistence.retry.RetryLogger
  • ubic.gemma.core.analysis.preprocess.filter.RowLevelFilter
  • ubic.gemma.core.analysis.preprocess.filter.RowMissingValueFilter
  • ubic.gemma.core.analysis.preprocess.filter.RowsWithSequencesFilter
  • ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisServiceImpl (implements ubic.gemma.persistence.service.analysis.expression.sampleCoexpression.SampleCoexpressionAnalysisService)
  • ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionMatrix (implements java.io.Serializable)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.ScoreValueObject (implements java.io.Serializable)
  • ubic.gemma.core.search.SearchResult<T> (implements java.lang.Comparable<T>)
  • ubic.gemma.core.search.SearchResultDisplayObject (implements java.lang.Comparable<T>)
  • ubic.gemma.core.search.SearchServiceImpl (implements org.springframework.beans.factory.InitializingBean, ubic.gemma.core.search.SearchService)
  • ubic.gemma.model.common.search.SearchSettings (implements java.io.Serializable)
  • ubic.gemma.model.common.search.SearchSettingsValueObject (implements java.io.Serializable)
  • ubic.gemma.core.analysis.sequence.SequenceBinUtils
  • ubic.gemma.core.analysis.sequence.SequenceManipulation
  • ubic.gemma.model.genome.sequenceAnalysis.SequenceSimilaritySearchResult (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
    • ubic.gemma.model.genome.sequenceAnalysis.BlatResult
  • ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject (implements java.io.Serializable)
  • ubic.gemma.core.analysis.sequence.SequenceWriter
  • ubic.gemma.persistence.util.ServiceBasedEntityConverter<O> (implements org.springframework.core.convert.converter.ConditionalGenericConverter)
    • ubic.gemma.persistence.util.ServiceBasedValueObjectConverter<O,VO> (implements org.springframework.core.convert.converter.ConditionalGenericConverter)
  • ubic.gemma.core.config.Settings
  • ubic.gemma.core.config.SettingsConfig
  • ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
  • ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
  • ubic.gemma.core.analysis.sequence.ShellDelegatingBlat (implements ubic.gemma.core.analysis.sequence.Blat)
  • ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderServiceImpl (implements ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService)
  • ubic.gemma.core.loader.genome.SimpleFastaCmd (implements ubic.gemma.core.loader.genome.FastaCmd)
  • ubic.gemma.core.search.lucene.SimpleHTMLFormatter (implements org.apache.lucene.search.highlight.Formatter)
  • ubic.gemma.core.search.lucene.SimpleMarkdownFormatter (implements org.apache.lucene.search.highlight.Formatter)
  • ubic.gemma.core.util.SimpleThreadFactory (implements java.util.concurrent.ThreadFactory)
  • ubic.gemma.model.genome.gene.phenotype.valueObject.SimpleTreeValueObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • ubic.gemma.persistence.util.Sort (implements ubic.gemma.persistence.util.PropertyMapping)
  • ubic.gemma.core.analysis.preprocess.SplitExperimentServiceImpl (implements ubic.gemma.core.analysis.preprocess.SplitExperimentService)
  • ubic.gemma.core.context.SpringContextUtils
  • ubic.gemma.model.expression.experiment.Statement.Factory
  • ubic.gemma.persistence.cache.StaticCacheKeyLock (implements ubic.gemma.persistence.cache.CacheKeyLock)
  • ubic.gemma.core.profiling.StopWatchUtils
  • ubic.gemma.core.profiling.StopWatchUtils.StopWatchRegion (implements java.lang.AutoCloseable)
  • ubic.gemma.core.job.SubmittedTasksMaintenance
  • ubic.gemma.core.job.progress.SubmittedTaskValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.util.Subquery
  • ubic.gemma.persistence.util.Subquery.Alias
  • ubic.gemma.persistence.util.SubqueryUtils
  • ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException.SuspiciousValueResult
  • ubic.gemma.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.persistence.service.maintenance.TableMaintenanceUtilImpl (implements ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil)
  • ubic.gemma.core.job.TaskCommand (implements java.io.Serializable)
    • ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand
    • ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand
    • ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand
    • ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
      • ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand
    • ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand
    • ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand
    • ubic.gemma.core.tasks.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.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.notification.TaskMailUtilsImpl (implements ubic.gemma.core.job.notification.TaskMailUtils)
  • ubic.gemma.core.job.notification.TaskPostProcessingImpl (implements ubic.gemma.core.job.notification.TaskPostProcessing)
  • ubic.gemma.core.job.TaskResult (implements java.io.Serializable)
  • ubic.gemma.core.job.TaskRunningServiceImpl (implements org.springframework.beans.factory.DisposableBean, org.springframework.beans.factory.InitializingBean, ubic.gemma.core.job.TaskRunningService)
  • ubic.gemma.model.genome.Taxon (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.genome.Taxon.Factory
  • ubic.gemma.core.loader.genome.taxon.TaxonLoader
  • ubic.gemma.persistence.service.genome.taxon.TaxonUtils
  • ubic.gemma.core.ontology.jena.TGFVO
  • java.lang.Thread (implements java.lang.Runnable)
    • ubic.gemma.core.util.concurrent.GenericStreamConsumer
    • ubic.gemma.core.util.concurrent.ParsingStreamConsumer<T>
  • ubic.gemma.core.metrics.binder.ThreadPoolExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
  • ubic.gemma.core.metrics.binder.ThreadPoolTaskExecutorMetrics (implements io.micrometer.core.instrument.binder.MeterBinder)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • ubic.gemma.core.loader.entrez.pubmed.ESearchException
      • java.io.IOException
        • ubic.gemma.core.loader.expression.geo.service.IOExceptionWithRetry
      • ubic.gemma.core.datastructure.matrix.QuantitationMismatchException
        • ubic.gemma.core.datastructure.matrix.InferredQuantitationMismatchException
        • ubic.gemma.core.datastructure.matrix.SuspiciousValuesForQuantitationException
      • java.lang.RuntimeException
        • ubic.gemma.core.loader.util.AlreadyExistsInSystemException
        • ubic.gemma.core.association.phenotype.EntityNotFoundException
        • ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService.MigrationFailedException
        • ubic.gemma.core.loader.util.parser.FileFormatException
        • ubic.gemma.core.util.GemmaRestApiClientException
        • ubic.gemma.core.analysis.preprocess.PreprocessingException
          • ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException
            • ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException
            • ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException
            • ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException
          • ubic.gemma.core.analysis.preprocess.FailedToComputeSingularValueDecomposition
          • ubic.gemma.core.analysis.preprocess.filter.FilteringException
            • ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException
              • ubic.gemma.core.analysis.preprocess.InsufficientProbesException
              • ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException
            • ubic.gemma.core.analysis.preprocess.filter.NoRowsLeftAfterFilteringException
          • ubic.gemma.core.analysis.preprocess.QuantitationMismatchPreprocessingException
          • ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException
          • ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException
        • ubic.gemma.core.datastructure.matrix.QuantitationTypeConversionException
          • ubic.gemma.core.analysis.preprocess.UnsupportedQuantitationScaleConversionException
        • ubic.gemma.core.analysis.expression.coexpression.links.UnsuitableForAnalysisException
      • ubic.gemma.core.search.SearchException
        • ubic.gemma.core.search.BaseCodeOntologySearchException
        • ubic.gemma.core.search.source.HibernateSearchException
        • ubic.gemma.core.search.ParseSearchException
          • ubic.gemma.core.search.lucene.LuceneParseSearchException
        • ubic.gemma.core.search.SearchTimeoutException
      • ubic.gemma.core.analysis.preprocess.svd.SVDException
  • ubic.gemma.model.expression.biomaterial.Treatment.Factory
  • ubic.gemma.core.analysis.preprocess.TwoChannelMissingValuesImpl (implements ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues)
  • ubic.gemma.model.common.measurement.Unit (implements ubic.gemma.model.common.Identifiable, java.io.Serializable)
  • ubic.gemma.model.common.measurement.Unit.Factory
  • ubic.gemma.model.common.auditAndSecurity.User.Factory
  • ubic.gemma.model.common.auditAndSecurity.UserGroup.Factory
  • 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.model.genome.gene.phenotype.valueObject.ValidateEvidenceValueObject (implements java.io.Serializable)
  • ubic.gemma.persistence.util.ValueObjectConfig
  • ubic.gemma.core.analysis.report.WhatsNew
  • ubic.gemma.core.analysis.report.WhatsNewServiceImpl (implements ubic.gemma.core.analysis.report.WhatsNewService)
  • ubic.gemma.core.util.XMLUtils

Interface Hierarchy

• ubic.gemma.core.image.aba.AllenBrainAtlasService
• ubic.gemma.core.analysis.expression.AnalysisUtilService
• ubic.gemma.core.analysis.service.ArrayDesignAnnotationService
• ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService
• ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeHelperService
• ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService
• ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperService
• ubic.gemma.core.analysis.report.ArrayDesignReportService
• ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService
• ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingService
• ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService
• java.lang.AutoCloseable
  • ubic.gemma.persistence.cache.CacheKeyLock.LockAcquisition
• org.springframework.beans.factory.Aware
  • org.springframework.context.ApplicationContextAware
    • ubic.gemma.core.analysis.expression.diff.AnalysisSelectionAndExecutionService
• ubic.gemma.persistence.service.BaseDao<T>
  • ubic.gemma.persistence.service.analysis.AnalysisDao<T>
    • ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao<T>
      • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao
      • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDao
  • ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>
    • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
  • ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailDao
  • ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>
    • ubic.gemma.persistence.service.common.description.BibliographicReferenceDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
    • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDao
    • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao
    • ubic.gemma.persistence.service.genome.biosequence.BioSequenceDao
    • ubic.gemma.persistence.service.blacklist.BlacklistedEntityDao
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultDao
    • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorDao
    • ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao
    • ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.FilteringDao<O>)
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
      • ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.CachedFilteringDao<O>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
      • ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
      • ubic.gemma.persistence.service.common.description.DatabaseEntryDao
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.FactorValueDao
      • ubic.gemma.persistence.service.genome.GeneDao
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
      • ubic.gemma.persistence.service.genome.taxon.TaxonDao
    • ubic.gemma.persistence.service.expression.experiment.GeeqDao
    • ubic.gemma.persistence.service.genome.gene.GeneProductDao
    • ubic.gemma.persistence.service.genome.gene.GeneSetDao
  • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDao
  • ubic.gemma.persistence.service.BrowsingDao<T>
    • ubic.gemma.persistence.service.common.description.BibliographicReferenceDao (also extends ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
    • ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
    • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
  • ubic.gemma.persistence.service.genome.ChromosomeDao
  • ubic.gemma.persistence.service.association.coexpression.CoexpressionNodeDegreeDao
  • ubic.gemma.persistence.service.expression.biomaterial.CompoundDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.ContactDao
  • ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao<T>
    • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao
    • ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorDao
    • ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorDao
  • ubic.gemma.persistence.service.association.phenotype.DifferentialExpressionEvidenceDao
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDao
  • ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignDao
  • ubic.gemma.persistence.service.association.phenotype.ExperimentalEvidenceDao
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetDao
  • ubic.gemma.persistence.service.common.description.ExternalDatabaseDao
  • ubic.gemma.persistence.service.FilteringDao<O>
    • ubic.gemma.persistence.service.CachedFilteringDao<O>
      • ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
    • ubic.gemma.persistence.service.FilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledDao<O,VO>)
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao
      • ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO> (also extends ubic.gemma.persistence.service.CachedFilteringDao<O>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao<C>)
      • ubic.gemma.persistence.service.common.description.CharacteristicDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
      • ubic.gemma.persistence.service.common.description.DatabaseEntryDao
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDao (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetDao<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.FactorValueDao
      • ubic.gemma.persistence.service.genome.GeneDao
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeDao
      • ubic.gemma.persistence.service.genome.taxon.TaxonDao
  • ubic.gemma.persistence.service.association.Gene2GOAssociationDao
  • ubic.gemma.persistence.service.genome.gene.GeneAliasDao
  • ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisDao
  • ubic.gemma.persistence.service.association.phenotype.GenericEvidenceDao
  • ubic.gemma.persistence.service.association.phenotype.GenericExperimentDao
  • ubic.gemma.persistence.service.association.phenotype.LiteratureEvidenceDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao
  • ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDao
  • ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisDao
  • ubic.gemma.persistence.service.common.protocol.ProtocolDao
  • ubic.gemma.persistence.service.association.ReferenceAssociationDao
  • ubic.gemma.persistence.service.expression.experiment.StatementDao
  • ubic.gemma.persistence.service.common.measurement.UnitDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.UserDao
  • ubic.gemma.persistence.service.common.auditAndSecurity.UserGroupDao
• ubic.gemma.persistence.service.BaseReadOnlyService<O>
  • ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>
    • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
  • ubic.gemma.persistence.service.BaseImmutableService<O>
    • ubic.gemma.persistence.service.analysis.AnalysisService<T>
      • ubic.gemma.persistence.service.analysis.expression.diff.GeneDiffExMetaAnalysisService
      • ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>
        • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService (also extends ubic.gemma.persistence.service.BaseService<O>)
        • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService
    • ubic.gemma.persistence.service.common.auditAndSecurity.AuditTrailService
    • ubic.gemma.persistence.service.BaseService<O>
      • ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.biosequence.BioSequenceService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.common.auditAndSecurity.ContactService
      • ubic.gemma.persistence.service.auditAndSecurity.curation.CuratableService<C,VO> (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
      • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService (also extends ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisService<T>)
      • ubic.gemma.persistence.service.expression.experiment.ExperimentalDesignService
      • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSubSetService
      • ubic.gemma.persistence.service.common.description.ExternalDatabaseService
      • ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.gene.GeneProductService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    • ubic.gemma.persistence.service.common.description.BibliographicReferenceService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    • ubic.gemma.persistence.service.blacklist.BlacklistedEntityService (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationService
    • ubic.gemma.persistence.service.expression.biomaterial.CompoundService
    • ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO>)
    • ubic.gemma.persistence.service.association.Gene2GOAssociationService
    • ubic.gemma.persistence.service.association.phenotype.service.PhenotypeAssociationService
    • ubic.gemma.persistence.service.analysis.expression.pca.PrincipalComponentAnalysisService
    • ubic.gemma.persistence.service.common.protocol.ProtocolService
  • ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>
    • ubic.gemma.persistence.service.common.description.BibliographicReferenceService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    • ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    • ubic.gemma.persistence.service.expression.bioAssay.BioAssayService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.genome.biosequence.BioSequenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.blacklist.BlacklistedEntityService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
    • ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatResultService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.common.description.CharacteristicService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.FilteringService<O>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.auditAndSecurity.curation.CuratableService<C,VO> (also extends ubic.gemma.persistence.service.BaseService<O>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
      • ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.expression.experiment.GeeqService
    • ubic.gemma.persistence.service.genome.gene.GeneProductService (also extends ubic.gemma.persistence.service.BaseService<O>)
    • ubic.gemma.persistence.service.genome.gene.GeneSetService (also extends ubic.gemma.persistence.service.BaseService<O>)
  • ubic.gemma.persistence.service.expression.experiment.BioAssaySetService
  • ubic.gemma.persistence.service.genome.ChromosomeService
  • ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorService<T>
    • ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService
    • ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorService
    • ubic.gemma.persistence.service.expression.bioAssayData.RawExpressionDataVectorService
  • ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultService
  • ubic.gemma.persistence.service.FilteringService<O>
    • ubic.gemma.persistence.service.FilteringVoEnabledService<O,VO> (also extends ubic.gemma.persistence.service.BaseVoEnabledService<O,VO>)
      • ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.auditAndSecurity.curation.CuratableService<C,VO> (also extends ubic.gemma.persistence.service.BaseService<O>)
        • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService
        • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService
      • ubic.gemma.persistence.service.common.description.DatabaseEntryService (also extends ubic.gemma.persistence.service.BaseImmutableService<O>)
      • ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetService (also extends ubic.gemma.persistence.service.analysis.AnalysisResultSetService<K,O>)
      • ubic.gemma.persistence.service.expression.experiment.FactorValueService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.genome.gene.GeneService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.common.quantitationtype.QuantitationTypeService (also extends ubic.gemma.persistence.service.BaseService<O>)
      • ubic.gemma.persistence.service.genome.taxon.TaxonService (also extends ubic.gemma.persistence.service.BaseService<O>)
• ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperService
• ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationService
• ubic.gemma.core.analysis.sequence.Blat
• ubic.gemma.persistence.cache.CacheKeyLock
• java.util.concurrent.Callable<V>
  • ubic.gemma.core.job.Task<C>
    • 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.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.curation.CuratableDao<C>
  • ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao (also extends ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
  • ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao (also extends ubic.gemma.persistence.service.BrowsingDao<T>, ubic.gemma.persistence.service.CachedFilteringVoEnabledDao<O,VO>)
  • ubic.gemma.persistence.service.common.auditAndSecurity.curation.GenericCuratableDao
• ubic.gemma.core.analysis.report.DatabaseViewGenerator
• ubic.gemma.core.loader.expression.DataUpdater
• ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisHelperService
• ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerService
• ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultCache
• ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer
• ubic.gemma.core.analysis.expression.diff.DiffExMetaAnalyzerService
• ubic.gemma.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.expression.experiment.ExpressionExperimentPrePersistService
• ubic.gemma.core.analysis.report.ExpressionExperimentReportService
• ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSearchService
• ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetValueObjectHelper
• ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderService
• ubic.gemma.persistence.service.expression.experiment.FactorValueDeletion
• ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorService
• ubic.gemma.core.ontology.FactorValueOntologyService
• ubic.gemma.core.ontology.FactorValueOntologyUtils.StatementVisitor<U,E>
• org.springframework.beans.factory.FactoryBean<T>
  • ubic.gemma.core.context.AsyncFactoryBean<T>
• ubic.gemma.core.loader.genome.FastaCmd
• ubic.gemma.core.loader.util.fetcher.Fetcher
  • ubic.gemma.core.loader.util.fetcher.ArchiveFetcher
  • ubic.gemma.core.loader.util.fetcher.HttpArchiveFetcherInterface
• ubic.gemma.core.analysis.service.FileService<T>
  • ubic.gemma.core.analysis.service.JsonFileService<T>
  • ubic.gemma.core.analysis.service.TsvFileService<T>
    • ubic.gemma.core.analysis.service.ExpressionAnalysisResultSetFileService
    • ubic.gemma.core.analysis.service.ExpressionDataFileService
• ubic.gemma.core.util.GemmaRestApiClient
• ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse.Error
• ubic.gemma.core.util.GemmaRestApiClient.Response
  • ubic.gemma.core.util.GemmaRestApiClient.DataResponse
  • ubic.gemma.core.util.GemmaRestApiClient.EmptyResponse
  • ubic.gemma.core.util.GemmaRestApiClient.ErrorResponse
  • ubic.gemma.core.util.GemmaRestApiClient.Redirection
• ubic.gemma.model.common.GemmaSessionBackedValueObject
• ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchService
• ubic.gemma.persistence.service.genome.gene.GeneCoreService
• ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService
• ubic.gemma.core.analysis.expression.diff.GeneDiffExMetaAnalysisHelperService
• ubic.gemma.core.analysis.service.GeneMultifunctionalityPopulationService
• ubic.gemma.persistence.service.genome.gene.GeneSearchService
• ubic.gemma.core.search.GeneSetSearch
• ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelper
• ubic.gemma.persistence.service.association.coexpression.GeneTestedInCache
• ubic.gemma.core.loader.expression.geo.service.GeoBrowserService
• ubic.gemma.core.loader.expression.geo.service.GeoService
• ubic.gemma.core.search.getOntologyTermFormatter
• ubic.gemma.core.ontology.GoMetric
• org.springframework.security.provisioning.GroupManager
  • gemma.gsec.authentication.UserManager (also extends org.springframework.security.provisioning.UserDetailsManager)
    • ubic.gemma.core.security.authentication.UserManager
• ubic.gemma.core.search.Highlighter
  • ubic.gemma.core.search.lucene.LuceneHighlighter
  • ubic.gemma.core.search.OntologyHighlighter
• ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneService
• ubic.gemma.model.common.Identifiable
  • ubic.gemma.model.common.auditAndSecurity.Auditable (also extends gemma.gsec.model.Securable)
    • ubic.gemma.model.common.auditAndSecurity.curation.Curatable
  • ubic.gemma.model.common.Describable
• ubic.gemma.core.search.IndexerService
• ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisPersister
• ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisService
• ubic.gemma.core.util.MailEngine
• ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis
• ubic.gemma.core.analysis.preprocess.MeanVarianceService
• ubic.gemma.core.analysis.preprocess.MeanVarianceServiceHelper
• io.micrometer.core.instrument.binder.MeterBinder
  • ubic.gemma.core.job.TaskRunningService
• ubic.basecode.ontology.providers.OntologyService
  • ubic.gemma.core.ontology.providers.GeneOntologyService
• ubic.gemma.core.ontology.OntologyService
• ubic.gemma.core.analysis.preprocess.OutlierDetectionService
• ubic.gemma.core.analysis.service.OutlierFlaggingService
• ubic.gemma.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.core.job.progress.ProgressUpdateAppender.ProgressUpdateCallback
• ubic.gemma.persistence.util.PropertyMapping
• 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.SearchService.SearchResultMap
• ubic.gemma.core.search.SearchSource
  • ubic.gemma.core.search.FieldAwareSearchSource
• java.io.Serializable
  • org.hibernate.transform.ResultTransformer
    • ubic.gemma.persistence.hibernate.TypedResultTransformer<T>
  • gemma.gsec.model.Securable
    • ubic.gemma.model.common.auditAndSecurity.Auditable (also extends ubic.gemma.model.common.Identifiable)
      • ubic.gemma.model.common.auditAndSecurity.curation.Curatable
• ubic.gemma.core.loader.expression.simple.SimpleExpressionDataLoaderService
• ubic.gemma.core.loader.util.sdo.SourceDomainObjectGenerator
• ubic.gemma.core.analysis.preprocess.SplitExperimentService
• ubic.gemma.core.job.SubmittedTask
• ubic.gemma.core.analysis.preprocess.svd.SVDService
• ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelper
• ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil
• ubic.gemma.core.job.notification.TaskMailUtils
• ubic.gemma.core.job.notification.TaskPostProcessing
• ubic.gemma.core.analysis.preprocess.TwoChannelMissingValueHelperService
• ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues
• org.springframework.security.core.userdetails.UserDetailsService
  • org.springframework.security.provisioning.UserDetailsManager
    • gemma.gsec.authentication.UserManager (also extends org.springframework.security.provisioning.GroupManager)
      • ubic.gemma.core.security.authentication.UserManager
• gemma.gsec.authentication.UserService
  • ubic.gemma.core.security.authentication.UserService
• ubic.gemma.core.analysis.preprocess.VectorMergingService
• ubic.gemma.model.common.description.Versioned
• ubic.gemma.core.analysis.report.WhatsNewService

Annotation Type Hierarchy

• ubic.gemma.model.annotations.GemmaRestOnly (implements java.lang.annotation.Annotation)
• ubic.gemma.model.annotations.GemmaWebOnly (implements java.lang.annotation.Annotation)
• ubic.gemma.core.security.audit.IgnoreAudit (implements java.lang.annotation.Annotation)
• ubic.gemma.persistence.retry.Retryable (implements java.lang.annotation.Annotation)
• ubic.gemma.core.context.TestComponent (implements java.lang.annotation.Annotation)
• ubic.gemma.model.common.ValueObject (implements java.lang.annotation.Annotation)

Enum Hierarchy

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