All Classes
- AbaGene
- ABALinkOutValueObject
- AbstractAnalyzer
- AbstractArg
- AbstractArrayArg
- AbstractAsyncFactoryBean
- AbstractAuditable
- AbstractAuthenticatedCLI
- AbstractCLI
- AbstractCriteriaFilteringVoEnabledDao
- AbstractCuratableDao
- AbstractCuratableValueObject
- AbstractDao
- AbstractDescribable
- AbstractDesignElementDataVectorDao
- AbstractDesignElementDataVectorService
- AbstractDifferentialExpressionAnalyzer
- AbstractEntityArg
- AbstractEntityArgService
- AbstractEntityArrayArg
- AbstractExceptionMapper
- AbstractFactorValueValueObjectSerializer
- AbstractFetcher
- AbstractFileService
- AbstractFilteringVoEnabledDao
- AbstractFilteringVoEnabledDao.FilterablePropertyMeta
- AbstractFilteringVoEnabledService
- AbstractGemmaEndpoint
- AbstractGeoService
- AbstractMatrixRowPairAnalysis
- AbstractMeterRegistryConfigurer
- AbstractNoopFilteringVoEnabledDao
- AbstractOntologyResourceSimple
- AbstractPersister
- AbstractPersister.Caches
- AbstractQueryFilteringVoEnabledDao
- AbstractService
- AbstractSetListContainer
- AbstractTask
- AbstractVoEnabledDao
- AbstractVoEnabledService
- AccessDeniedExceptionMapper
- AclAdvice
- AclAfterCollectionCompSeqByArrayDesignFilter
- AclAfterCollectionDataVectorByExpressionExperimentFilter
- AclAfterCompSeqByArrayDesignFilter
- AclCriteriaUtils
- AclQueryUtils
- AffyChipTypeExtractor
- AffyDataFromCelCli
- AffyPowerToolsProbesetSummarize
- AffyProbeCollapseCli
- AffyProbeNameFilter
- AffyProbeNameFilter.Pattern
- AffyProbeReader
- AffyScanDateExtractor
- AgilentScanDateExtractor
- AlignmentBasedGeneMappingEvent
- AllenBrainAtlasService
- AllenBrainAtlasServiceImpl
- AlreadyExistsInSystemException
- AlternateName
- AlternateName.Factory
- Analysis
- AnalysisDao
- AnalysisResult
- AnalysisResultSet
- AnalysisResultSetDao
- AnalysisResultSetService
- AnalysisResultSetsWebService
- AnalysisResultSetValueObject
- AnalysisResultValueObject
- AnalysisSelectionAndExecutionService
- AnalysisSelectionAndExecutionServiceImpl
- AnalysisService
- AnalysisSuitabilityEvent
- AnalysisUtilService
- AnalysisUtilServiceImpl
- AnalysisValueObject
- AnalyticsApplicationEventListener
- AnalyticsProvider
- AnalyticsRequestEventListener
- AnchorTagUtil
- AnnotationAssociation
- AnnotationAssociation.Factory
- AnnotationAssociationDao
- AnnotationAssociationDaoImpl
- AnnotationAssociationService
- AnnotationAssociationServiceImpl
- AnnotationBasedGeneMappingEvent
- AnnotationController
- AnnotationEvent
- AnnotationsWebService
- AnnotationsWebService.AnnotationSearchResultValueObject
- AnnotationValueObject
- ArchiveFetcher
- Arg
- ArgUtils
- ArrayDesign
- ArrayDesign.Factory
- ArrayDesignAddCommand
- ArrayDesignAlternativePopulateCli
- ArrayDesignAnalysisEvent
- ArrayDesignAnnotationFileCli
- ArrayDesignAnnotationService
- ArrayDesignAnnotationService.OutputType
- ArrayDesignAnnotationServiceImpl
- ArrayDesignAuditTrailCleanupCli
- ArrayDesignBioSequenceDetachCli
- ArrayDesignBlatCli
- ArrayDesignController
- ArrayDesignControllerImpl
- ArrayDesignDao
- ArrayDesignDaoImpl
- ArrayDesignFormController
- ArrayDesignGeneMappingEvent
- ArrayDesignGroupingTag
- ArrayDesignHtmlUtil
- ArrayDesignIdentifierByNameEndpoint
- ArrayDesignMapResultService
- ArrayDesignMapResultServiceImpl
- ArrayDesignMapSummaryCli
- ArrayDesignMergeCli
- ArrayDesignMergeEvent
- ArrayDesignMergeHelperService
- ArrayDesignMergeHelperServiceImpl
- ArrayDesignMergeService
- ArrayDesignMergeServiceImpl
- ArrayDesignParser
- ArrayDesignPersister
- ArrayDesignProbeCleanupCLI
- ArrayDesignProbeMapperCli
- ArrayDesignProbeMapperController
- ArrayDesignProbeMapperService
- ArrayDesignProbeMapperServiceImpl
- ArrayDesignProbeMapperTaskImpl
- ArrayDesignProbeMapTaskCommand
- ArrayDesignProbeRenamerCli
- ArrayDesignProbeRenamingEvent
- ArrayDesignPropertyEditor
- ArrayDesignRepeatAnalysisEvent
- ArrayDesignRepeatScanCli
- ArrayDesignRepeatScanController
- ArrayDesignRepeatScanTask
- ArrayDesignRepeatScanTaskCommand
- ArrayDesignRepeatScanTaskImpl
- ArrayDesignReportService
- ArrayDesignReportServiceImpl
- ArrayDesignSequenceAlignmentService
- ArrayDesignSequenceAlignmentServiceImpl
- ArrayDesignSequenceAnalysisEvent
- ArrayDesignSequenceAssociationCli
- ArrayDesignSequenceManipulatingCli
- ArrayDesignSequenceProcessingService
- ArrayDesignSequenceProcessingServiceImpl
- ArrayDesignSequenceRemoveEvent
- ArrayDesignSequenceUpdateEvent
- ArrayDesignService
- ArrayDesignServiceImpl
- ArrayDesignsForExperimentCache
- ArrayDesignSubsumeCheckEvent
- ArrayDesignSubsumptionTesterCli
- ArrayDesignUsedEndpoint
- ArrayDesignValueObject
- ArrayDesignValueObjectExt
- ArrayExpressUtil
- AssayViewTag
- AsyncFactoryBean
- AsyncFactoryBeanUtils
- Auditable
- AuditableObject
- AuditAction
- AuditAdvice
- AuditController
- AuditEvent
- AuditEvent.Factory
- AuditEventDao
- AuditEventDaoImpl
- AuditEventService
- AuditEventServiceImpl
- AuditEventType
- AuditEventValueObject
- AuditTrail
- AuditTrail.Factory
- AuditTrailDao
- AuditTrailDaoImpl
- AuditTrailService
- AuditTrailServiceImpl
- AuthenticationBasedUserIdRetrievalStrategy
- AuthenticationExceptionMapper
- AutomatedAnnotationEvent
- BaseCodeOntologySearchException
- BaseController
- BaseDao
- BaseExpressionDataMatrix
- BaseFormController
- BaseImmutableService
- BaselineSelection
- BaseReadOnlyService
- BaseScanDateExtractor
- BaseService
- BaseValueObject
- BaseVoEnabledDao
- BaseVoEnabledService
- BashCompletionGenerator
- BasicLineMapParser
- BasicLineParser
- BatchConfound
- BatchConfoundUtils
- BatchCorrectionEvent
- BatchEffectDetails
- BatchEffectPopulationCli
- BatchEffectType
- BatchEffectType
- BatchInfoFetchController
- BatchInfoFetchTask
- BatchInfoFetchTaskCommand
- BatchInfoFetchTaskImpl
- BatchInfoParser
- BatchInfoPopulationException
- BatchInfoPopulationHelperService
- BatchInfoPopulationHelperServiceImpl
- BatchInfoPopulationService
- BatchInfoPopulationServiceImpl
- BatchInformationEvent
- BatchInformationFetchingEvent
- BatchInformationMissingEvent
- BatchProblemsUpdateEvent
- BeanInitializationTimeMonitor
- BeanNameGenerator
- BibliographicPhenotypesValueObject
- BibliographicReference
- BibliographicReference.Factory
- BibliographicReferenceController
- BibliographicReferenceControllerImpl
- BibliographicReferenceDao
- BibliographicReferenceDaoImpl
- BibliographicReferenceService
- BibliographicReferenceServiceImpl
- BibliographicReferenceValueObject
- BibRefAnnotation
- BibRefUpdaterCli
- BioAssay
- BioAssay.Factory
- BioAssayController
- BioAssayDao
- BioAssayDaoImpl
- BioAssayDimension
- BioAssayDimension.Factory
- BioAssayDimensionDao
- BioAssayDimensionDaoImpl
- BioAssayDimensionService
- BioAssayDimensionServiceImpl
- BioAssayDimensionValueObject
- BioAssayOutlierProcessingTask
- BioAssayOutlierProcessingTaskCommand
- BioAssayOutlierProcessingTaskImpl
- BioAssayService
- BioAssayServiceImpl
- BioAssaySet
- BioAssaySetService
- BioAssaySetServiceImpl
- BioAssayValueObject
- BiomartEnsembleNcbiParser
- BiomartEnsemblNcbiFetcher
- BiomartEnsemblNcbiObjectGenerator
- BioMaterial
- BioMaterial.Factory
- BioMaterialController
- BioMaterialDao
- BioMaterialDaoImpl
- BioMaterialMappingUpdate
- BioMaterialService
- BioMaterialServiceImpl
- BioMaterialValueObject
- BioSequence
- BioSequence.Factory
- BioSequence2GeneProduct
- BioSequenceCleanupCli
- BioSequenceDao
- BioSequenceDaoImpl
- BioSequenceService
- BioSequenceServiceImpl
- BioSequenceValueObject
- BlacklistCli
- BlacklistedEntity
- BlacklistedEntityDao
- BlacklistedEntityDaoImpl
- BlacklistedEntityService
- BlacklistedEntityServiceImpl
- BlacklistedExperiment
- BlacklistedPlatform
- BlacklistedValueObject
- Blat
- BlatAssociation
- BlatAssociation.Factory
- BlatAssociationDao
- BlatAssociationDaoImpl
- BlatAssociationScorer
- BlatAssociationService
- BlatAssociationServiceImpl
- BlatResult
- BlatResult.Factory
- BlatResult2Psl
- BlatResultDao
- BlatResultDaoImpl
- BlatResultParser
- BlatResultService
- BlatResultServiceImpl
- BlatResultTrackController
- BlatResultValueObject
- BooleanVectorValueObject
- BrowsingDao
- BuildInfo
- BusinessKey
- CacheControl
- CacheControlHeaderDecorator
- CacheControls
- CachedFilteringDao
- CachedFilteringVoEnabledDao
- CacheMonitor
- CacheMonitorImpl
- CacheUtils
- CacheUtils.Lock
- ChannelUtils
- Characteristic
- Characteristic.Factory
- CharacteristicBrowserController
- CharacteristicConverter
- CharacteristicDao
- CharacteristicDao.CharacteristicUsageFrequency
- CharacteristicDaoImpl
- CharacteristicService
- CharacteristicServiceImpl
- CharacteristicUpdateCommand
- CharacteristicUpdateTask
- CharacteristicUpdateTaskImpl
- CharacteristicUtils
- CharacteristicValueObject
- Chromosome
- ChromosomeDao
- ChromosomeDaoImpl
- ChromosomeFeature
- ChromosomeLocation
- ChromosomeService
- ChromosomeServiceImpl
- ChromosomeUtil
- CitationValueObject
- ClassConverter
- CLI
- ClientIdRetrievalStrategy
- CoexpCorrelationDistribution
- CoexpCorrelationDistribution.Factory
- CoexpressionAnalysis
- CoexpressionAnalysis.Factory
- CoexpressionAnalysisDao
- CoexpressionAnalysisDaoImpl
- CoexpressionAnalysisService
- CoexpressionAnalysisServiceImpl
- CoexpressionCache
- CoexpressionCacheImpl
- CoexpressionCacheValueObject
- CoexpressionDao
- CoexpressionDaoImpl
- CoexpressionMetaValueObject
- CoexpressionNodeDegreeDao
- CoexpressionNodeDegreeDaoImpl
- CoexpressionSearchCommand
- CoexpressionSearchController
- CoexpressionService
- CoexpressionServiceImpl
- CoexpressionSummaryValueObject
- CoexpressionValueObject
- CoexpressionValueObjectExt
- CoexSearchTaskCommand
- ComBat
- CommentedEvent
- CommonPersister
- CommonQueries
- CommonsMultipartFile
- CommonsMultipartMonitoredResolver
- CompletionGenerator
- CompositeClientIdRetrievalStrategy
- CompositeSearchSource
- CompositeSequence
- CompositeSequence.Factory
- CompositeSequenceArg
- CompositeSequenceArgService
- CompositeSequenceArrayArg
- CompositeSequenceController
- CompositeSequenceDao
- CompositeSequenceDaoImpl
- CompositeSequenceGeneMapperService
- CompositeSequenceIdArg
- CompositeSequenceMapSummary
- CompositeSequenceMapValueObject
- CompositeSequenceNameArg
- CompositeSequenceParser
- CompositeSequenceService
- CompositeSequenceServiceImpl
- CompositeSequenceValueObject
- Compound
- Compound.Factory
- CompoundDao
- CompoundDaoImpl
- CompoundService
- CompoundServiceImpl
- ConfigurationCookie
- ConfigurationLinter
- Constants
- ConstantsTag
- ConstantsTei
- Contact
- Contact.Factory
- ContactDao
- ContactDaoImpl
- ContactService
- ContactServiceImpl
- ContrastResult
- ContrastResult.Factory
- ContrastResultValueObject
- ContrastsValueObject
- ContrastVO
- ControllerUtils
- Converter
- CorsFilter
- CtdDatabaseImporterCli
- Curatable
- CuratableDao
- CuratableService
- CurationDetails
- CurationDetailsEvent
- CurationNoteUpdateEvent
- CustomModelResolver
- CustomModelResolverRegistrationListener
- CustomRssViewer
- DataAddedEvent
- DataAnalysisEvidence
- DatabaseBackedGeneSetValueObject
- DatabaseEntry
- DatabaseEntry.Factory
- DatabaseEntryArg
- DatabaseEntryArgService
- DatabaseEntryArrayArg
- DatabaseEntryDao
- DatabaseEntryDaoImpl
- DatabaseEntryIdArg
- DatabaseEntryService
- DatabaseEntryServiceImpl
- DatabaseEntryStringArg
- DatabaseEntryTag
- DatabaseEntryValueObject
- DatabaseSearchSource
- DatabaseType
- DatabaseViewGenerator
- DatabaseViewGeneratorCLI
- DatabaseViewGeneratorImpl
- DataFileFetcher
- DataRemovedEvent
- DataReplacedEvent
- DatasetArg
- DatasetArgService
- DatasetArrayArg
- DatasetCombiner
- DatasetFetcher
- DatasetIdArg
- DatasetStringArg
- DatasetsWebService
- DatasetsWebService.AnnotationWithUsageStatisticsValueObject
- DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
- DatasetsWebService.CategoryWithUsageStatisticsValueObject
- DatasetsWebService.ExpressionExperimentWithSearchResultValueObject
- DatasetsWebService.OntologyTermValueObject
- DatasetsWebService.TaxonWithUsageStatisticsValueObject
- DatasetsWebService.UsageStatistics
- DataUpdater
- DataUpdaterImpl
- DataVector
- DataVectorValueObject
- DEDVController
- DEDVfromEEIDGeneIDEndpoint
- DEDVRankEndpoint
- DefaultHighlighter
- DeleteDiffExCli
- DeleteEvidenceCLI
- DeleteExperimentsCli
- Describable
- DescribableComparator
- DesignElementDataVector
- DesignElementDataVectorDao
- DesignMatrixRowValueObject
- DesignMatrixRowValueObject.Factory
- DgaDatabaseImporterCli
- DifferentialExpressionAnalysis
- DifferentialExpressionAnalysis.Factory
- DifferentialExpressionAnalysisCli
- DifferentialExpressionAnalysisConfig
- DifferentialExpressionAnalysisController
- DifferentialExpressionAnalysisDao
- DifferentialExpressionAnalysisEvent
- DifferentialExpressionAnalysisHelperService
- DifferentialExpressionAnalysisHelperServiceImpl
- DifferentialExpressionAnalysisRemoveTaskCommand
- DifferentialExpressionAnalysisResult
- DifferentialExpressionAnalysisResult.Factory
- DifferentialExpressionAnalysisResultComparator
- DifferentialExpressionAnalysisResultComparator.Factory
- DifferentialExpressionAnalysisResultSetValueObject
- DifferentialExpressionAnalysisResultSetVisualizationValueObject
- DifferentialExpressionAnalysisResultValueObject
- DifferentialExpressionAnalysisService
- DifferentialExpressionAnalysisServiceImpl
- DifferentialExpressionAnalysisTask
- DifferentialExpressionAnalysisTaskCommand
- DifferentialExpressionAnalysisTaskImpl
- DifferentialExpressionAnalysisUtil
- DifferentialExpressionAnalysisValueObject
- DifferentialExpressionAnalyzerInfo
- DifferentialExpressionAnalyzerService
- DifferentialExpressionAnalyzerServiceImpl
- DifferentialExpressionAnalyzerServiceImpl.AnalysisType
- DifferentialExpressionEvidence
- DifferentialExpressionEvidence.Factory
- DifferentialExpressionEvidenceDao
- DifferentialExpressionEvidenceDaoImpl
- DifferentialExpressionFileUtils
- DifferentialExpressionGenesConditionsValueObject
- DifferentialExpressionMetaAnalysisValueObject
- DifferentialExpressionProbeResultEndpoint
- DifferentialExpressionResultCache
- DifferentialExpressionResultCacheImpl
- DifferentialExpressionResultDao
- DifferentialExpressionResultDaoImpl
- DifferentialExpressionResultService
- DifferentialExpressionResultServiceImpl
- DifferentialExpressionSearchController
- DifferentialExpressionSearchTask
- DifferentialExpressionSearchTaskCommand
- DifferentialExpressionSearchTaskImpl
- DifferentialExpressionSuitabilityEvent
- DifferentialExpressionValueObject
- DiffExAnalyzer
- DiffExMetaAnalyzerController
- DiffExMetaAnalyzerService
- DiffExMetaAnalyzerServiceImpl
- DiffExMetaAnalyzerTask
- DiffExMetaAnalyzerTaskCommand
- DiffExMetaAnalyzerTaskImpl
- DiffExpressionEvidenceValueObject
- DiffExpressionSearchCommand
- DiffExpressionSelectedFactorCommand
- DiffExprGeneSearchResult
- DiffExResultSetSummaryValueObject
- Direction
- DirectionConverter
- DoesNotNeedAttentionEvent
- DoublePointConverter
- DoubleVectorValueObject
- DummyMailSender
- DumpsValueObject
- EE2CAclQueryUtils
- EhCache24Metrics
- EhcacheConfig
- Eigenvalue
- Eigenvalue.Factory
- Eigenvector
- Eigenvector.Factory
- EmailNotificationContext
- EmptyController
- EmptyExpressionMatrix
- Ensembl2NcbiValueObject
- EntityArgService
- EntityDelegator
- EntityNotFoundException
- EntityNotFoundException
- EntityNotFoundException
- EntityNotFoundExceptionMapper
- EntityUtils
- EnvironmentProfiles
- ESearchException
- ESearchXMLParser
- EutilFetch
- EutilFetch.Mode
- EvidenceFilter
- EvidenceImporterAbstractCLI
- EvidenceImporterCLI
- EvidenceSecurityValueObject
- EvidenceSourceValueObject
- EvidenceValueObject
- ExceptionMapperUtils
- ExceptionTag
- ExcludeArg
- ExecutingTask
- ExecutingTask.TaskLifecycleHandler
- ExperimentalDesign
- ExperimentalDesign.Factory
- ExperimentalDesignController
- ExperimentalDesignDao
- ExperimentalDesignDaoImpl
- ExperimentalDesignImportCli
- ExperimentalDesignImporter
- ExperimentalDesignImporterImpl
- ExperimentalDesignService
- ExperimentalDesignServiceImpl
- ExperimentalDesignUpdatedEvent
- ExperimentalDesignUtils
- ExperimentalDesignViewCli
- ExperimentalDesignVisualizationService
- ExperimentalDesignVisualizationServiceImpl
- ExperimentalDesignWriter
- ExperimentalDesignWriterCLI
- ExperimentalEvidence
- ExperimentalEvidence.Factory
- ExperimentalEvidenceDao
- ExperimentalEvidenceDaoImpl
- ExperimentalEvidenceValueObject
- ExperimentalFactor
- ExperimentalFactor.Factory
- ExperimentalFactorDao
- ExperimentalFactorDaoImpl
- ExperimentalFactorService
- ExperimentalFactorServiceImpl
- ExperimentalFactorValueObject
- ExperimentalFactorValueWebUIObject
- ExperimentAnnotationEndpoint
- ExperimentCoexpressionLink
- ExperimentDEDVEndpoint
- ExperimentExpressionLevelsValueObject
- ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
- ExperimentExpressionLevelsValueObject.VectorElementValueObject
- ExperimentIDbyTaxonEndpoint
- ExperimentIdEndpoint
- ExperimentNameEndpoint
- ExperimentNumSamplesEndpoint
- ExperimentPlatformSwitchHelperService
- ExperimentQCTag
- ExperimentSetListContainer
- ExpLevelConsolidationArg
- ExpressionAnalysis
- ExpressionAnalysisResultSet
- ExpressionAnalysisResultSet.Factory
- ExpressionAnalysisResultSetArg
- ExpressionAnalysisResultSetArgService
- ExpressionAnalysisResultSetDao
- ExpressionAnalysisResultSetDaoImpl
- ExpressionAnalysisResultSetFileService
- ExpressionAnalysisResultSetFileServiceImpl
- ExpressionAnalysisResultSetService
- ExpressionAnalysisResultSetServiceImpl
- ExpressionDataBooleanMatrix
- ExpressionDataCorrMatCli
- ExpressionDataDoubleMatrix
- ExpressionDataDoubleMatrixUtil
- ExpressionDataFileService
- ExpressionDataFileServiceImpl
- ExpressionDataFileUploadController
- ExpressionDataIntegerMatrix
- ExpressionDataMatrix
- ExpressionDataMatrixBuilder
- ExpressionDataMatrixColumnSort
- ExpressionDataMatrixRowElement
- ExpressionDataMatrixService
- ExpressionDataMatrixServiceImpl
- ExpressionDataMatrixWriterCLI
- ExpressionDataStringMatrix
- ExpressionDataSVD
- ExpressionDataWriterUtils
- ExpressionExperiment
- ExpressionExperiment.Factory
- ExpressionExperimentAnalysisEvent
- ExpressionExperimentBatchCorrectionService
- ExpressionExperimentBatchCorrectionServiceImpl
- ExpressionExperimentBibRefFinder
- ExpressionExperimentController
- ExpressionExperimentDao
- ExpressionExperimentDaoImpl
- ExpressionExperimentDataFetchCommand
- ExpressionExperimentDataFetchController
- ExpressionExperimentDataFileGeneratorCli
- ExpressionExperimentDetailsValueObject
- ExpressionExperimentEditValueObject
- ExpressionExperimentExperimentalFactorValueObject
- ExpressionExperimentFilter
- ExpressionExperimentFormController
- ExpressionExperimentLoadController
- ExpressionExperimentLoadTask
- ExpressionExperimentLoadTaskCommand
- ExpressionExperimentLoadTaskImpl
- ExpressionExperimentManipulatingCLI
- ExpressionExperimentMetaFileType
- ExpressionExperimentPlatformSwitchCli
- ExpressionExperimentPlatformSwitchEvent
- ExpressionExperimentPlatformSwitchService
- ExpressionExperimentPrePersistService
- ExpressionExperimentPrePersistServiceImpl
- ExpressionExperimentPrimaryPubCli
- ExpressionExperimentQCController
- ExpressionExperimentQCUtils
- ExpressionExperimentReportGenerationController
- ExpressionExperimentReportService
- ExpressionExperimentReportServiceImpl
- ExpressionExperimentReportTask
- ExpressionExperimentReportTaskCommand
- ExpressionExperimentReportTaskImpl
- ExpressionExperimentSearchService
- ExpressionExperimentSearchServiceImpl
- ExpressionExperimentService
- ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm
- ExpressionExperimentServiceImpl
- ExpressionExperimentSet
- ExpressionExperimentSet.Factory
- ExpressionExperimentSetController
- ExpressionExperimentSetDao
- ExpressionExperimentSetDaoImpl
- ExpressionExperimentSetIDsEndpoint
- ExpressionExperimentSetService
- ExpressionExperimentSetServiceImpl
- ExpressionExperimentSetValueObject
- ExpressionExperimentSetValueObjectHelper
- ExpressionExperimentSetValueObjectHelperImpl
- ExpressionExperimentSubSet
- ExpressionExperimentSubSet.Factory
- ExpressionExperimentSubSetDao
- ExpressionExperimentSubSetDaoImpl
- ExpressionExperimentSubSetService
- ExpressionExperimentSubSetServiceImpl
- ExpressionExperimentSubsetValueObject
- ExpressionExperimentUpdateFromGEOEvent
- ExpressionExperimentUploadResponse
- ExpressionExperimentValueObject
- ExpressionExperimentVectorManipulatingService
- ExpressionExperimentVectorMergeEvent
- ExpressionExperimentVisualizationCommand
- ExpressionPersister
- ExpressionProfileDataObject
- ExternalDatabase
- ExternalDatabase.Factory
- ExternalDatabaseAdderCli
- ExternalDatabaseDao
- ExternalDatabaseDaoImpl
- ExternalDatabaseEvidenceImporterAbstractCLI
- ExternalDatabaseOverviewCli
- ExternalDatabases
- ExternalDatabaseService
- ExternalDatabaseServiceImpl
- ExternalDatabaseStatisticsValueObject
- ExternalDatabaseUpdaterCli
- ExternalDatabaseUtils
- ExternalDatabaseValueObject
- ExternalFileGeneLoaderCLI
- ExternalFileGeneLoaderService
- ExternalFileGeneLoaderServiceImpl
- FactorAssociatedAnalysisResultSet
- FactorProfile
- FactorType
- FactorValue
- FactorValue.Factory
- FactorValueArg
- FactorValueArrayArg
- FactorValueBasicValueObject
- FactorValueBasicValueObjectSerializer
- FactorValueComparator
- FactorValueDao
- FactorValueDaoImpl
- FactorValueDeletion
- FactorValueDeletionImpl
- FactorValueIdArg
- FactorValueMigratorCLI
- FactorValueMigratorService
- FactorValueMigratorService.Migration
- FactorValueMigratorService.MigrationFailedException
- FactorValueMigratorService.MigrationResult
- FactorValueMigratorServiceImpl
- FactorValueNeedsAttentionEvent
- FactorValueOntologyService
- FactorValueOntologyService.OntologyStatement
- FactorValueOntologyServiceImpl
- FactorValueOntologyUtils
- FactorValueOntologyUtils.Annotation
- FactorValueOntologyUtils.AnnotationIds
- FactorValueOntologyUtils.StatementVisitor
- FactorValueService
- FactorValueServiceImpl
- FactorValueUtils
- FactorValueValueArg
- FactorValueValueObject
- FactorValueValueObjectSerializer
- FactorValueVector
- FailedBatchInformationFetchingEvent
- FailedBatchInformationMissingEvent
- FailedDataReplacedEvent
- FailedDifferentialExpressionAnalysisEvent
- FailedLinkAnalysisEvent
- FailedMeanVarianceUpdateEvent
- FailedMissingValueAnalysisEvent
- FailedMultipartHttpServletRequest
- FailedPCAAnalysisEvent
- FailedProcessedVectorComputationEvent
- FailedSampleCorrelationAnalysisEvent
- FailedToComputeSingularValueDecomposition
- FastaCmd
- FastaParser
- FASTQHeadersPresentButNotUsableException
- FeedReader
- Fetcher
- FieldAwareSearchSource
- FileFormatException
- FileService
- FileUpload
- FileUploadController
- FileUploadUtil
- FileUtils
- Filter
- Filter.Operator
- FilterArg
- FilterArg.Filter
- FilterArgBaseListener
- FilterArgLexer
- FilterArgListener
- FilterArgParser
- FilterArgParser.ClauseContext
- FilterArgParser.CollectionContext
- FilterArgParser.CollectionOperatorContext
- FilterArgParser.DisjunctionContext
- FilterArgParser.FilterContext
- FilterArgParser.OperatorContext
- FilterArgParser.ScalarContext
- FilterArgParser.SubClauseContext
- FilterConfig
- FilterCriteriaUtils
- FilteredAndPaginatedResponseDataObject
- FilteredResponseDataObject
- FilteringDao
- FilteringException
- FilteringService
- FilteringVoEnabledDao
- FilteringVoEnabledService
- FilterQueryUtils
- Filters
- FiltersUtils
- FindObsoleteTermsCli
- FishCompletionGenerator
- FreeTextExpressionExperimentResultsValueObject
- FreeTextGeneResultsValueObject
- FtpArchiveFetcher
- FtpFetcher
- Geeq
- GeeqAdminValueObject
- GeeqCli
- GeeqDao
- GeeqDaoImpl
- GeeqEvent
- GeeqService
- GeeqService.ScoreMode
- GeeqServiceImpl
- GeeqValueObject
- GemmaClassicHomePageController
- GemmaCLI
- GemmaCLI.CommandGroup
- GemmaOntologyService
- GemmaRestOnly
- GemmaSessionBackedValueObject
- GemmaWebOnly
- Gene
- Gene.Factory
- Gene2CsStatus
- Gene2GeneAssociation
- Gene2GeneCoexpression
- Gene2GeneIdAssociation
- Gene2GOAssociation
- Gene2GOAssociation.Factory
- Gene2GOAssociationDao
- Gene2GOAssociationDaoImpl
- Gene2GOAssociationService
- Gene2GOAssociationServiceImpl
- Gene2GOdescriptionEndpoint
- Gene2GoTermEndpoint
- Gene2OntologyEntryAssociation
- Gene2OntologyEntryAssociationImpl
- Gene2ProbeEndpoint
- GeneAlias
- GeneAlias.Factory
- GeneAliasDao
- GeneAliasDaoImpl
- GeneAnyIdArg
- GeneArg
- GeneArgService
- GeneArrayArg
- GeneByNCBIIdEndpoint
- GeneCoexpressedGenes
- GeneCoexpressionEndpoint
- GeneCoexpressionNodeDegree
- GeneCoexpressionNodeDegree.Factory
- GeneCoexpressionNodeDegreeValueObject
- GeneCoexpressionSearchEndpoint
- GeneCoexpressionSearchService
- GeneCoexpressionSearchServiceImpl
- GeneCoexpressionTestedIn
- GeneController
- GeneCoreService
- GeneDao
- GeneDaoImpl
- GeneDetailsByGeneIDEndpoint
- GeneDifferentialExpressionMetaAnalysis
- GeneDifferentialExpressionMetaAnalysis.Factory
- GeneDifferentialExpressionMetaAnalysisDetailValueObject
- GeneDifferentialExpressionMetaAnalysisResult
- GeneDifferentialExpressionMetaAnalysisResult.Factory
- GeneDifferentialExpressionMetaAnalysisResultValueObject
- GeneDifferentialExpressionMetaAnalysisSummaryValueObject
- GeneDifferentialExpressionService
- GeneDifferentialExpressionServiceImpl
- GeneDiffExMetaAnalysisDao
- GeneDiffExMetaAnalysisDaoImpl
- GeneDiffExMetaAnalysisHelperService
- GeneDiffExMetaAnalysisHelperServiceImpl
- GeneDiffExMetaAnalysisService
- GeneDiffExMetaAnalysisServiceImpl
- GeneEnsemblIdArg
- GeneEvidenceValueObject
- GeneExpressionProfile
- GeneIDbyTaxonEndpoint
- GeneIdEndpoint
- GeneMappingSummary
- GeneMultifunctionalityPopulationService
- GeneMultifunctionalityPopulationServiceImpl
- GeneNameEndpoint
- GeneNcbiIdArg
- GeneOntologyService
- GeneOntologyServiceImpl
- GeneOntologyServiceImpl.GOAspect
- GeneOntologyTermValueObject
- GeneOverlapEndpoint
- GenePickerController
- GeneProduct
- GeneProduct.Factory
- GeneProductDao
- GeneProductDaoImpl
- GeneProductService
- GeneProductServiceImpl
- GeneProductValueObject
- GeneralSearchController
- GeneralSearchController.SearchResultValueObject
- GeneralSearchControllerImpl
- GeneralType
- GenericCuratableDao
- GenericCuratableDaoImpl
- GenericEvidence
- GenericEvidence.Factory
- GenericEvidenceDao
- GenericEvidenceDaoImpl
- GenericEvidenceValueObject
- GenericExperiment
- GenericExperiment.Factory
- GenericExperimentDao
- GenericExperimentDaoImpl
- GenericGenelistDesignGenerator
- GenericMeterRegistryConfigurer
- GenericScanFileDateExtractor
- GenericStreamConsumer
- GeneSearchService
- GeneSearchServiceImpl
- GeneService
- GeneServiceImpl
- GeneSet
- GeneSet.Factory
- GeneSetController
- GeneSetDao
- GeneSetDaoImpl
- GeneSetListContainer
- GeneSetMember
- GeneSetMember.Factory
- GeneSetMemberDaoImpl
- GeneSetSearch
- GeneSetSearchImpl
- GeneSetService
- GeneSetServiceImpl
- GeneSetValueObject
- GeneSetValueObjectHelper
- GeneSetValueObjectHelperImpl
- GeneSymbolArg
- GeneSymbolComparator
- GeneTestedInCache
- GeneTestedInCacheImpl
- GeneValueObject
- GeneWebService
- GenomePersister
- GeoBrowser
- GeoBrowserService
- GeoBrowserServiceImpl
- GeoChannel
- GeoChannel.ChannelMolecule
- GeoConstants
- GeoContact
- GeoConverter
- GeoConverterImpl
- GeoData
- GeoDataset
- GeoDataset.ExperimentType
- GeoDataset.PlatformType
- GeoDataset.SampleType
- GeoDataset.ValueType
- GeoDomainObjectGenerator
- GeoDomainObjectGeneratorLocal
- GeoFamilyParser
- GeoFetcher
- GeoGrabberCli
- GeoParseResult
- GeoPlatform
- GeoRecord
- GeoRecordBrowserController
- GeoReplication
- GeoReplication.ReplicationType
- GeoSample
- GeoSample.LibraryStrategy
- GeoSampleCorrespondence
- GeoSeries
- GeoSeries.SeriesType
- GeoService
- GeoServiceImpl
- GeoSubset
- GeoUtil
- GeoValues
- GeoVariable
- GeoVariable.VariableType
- getOntologyTermFormatter
- GOEvidenceCode
- GOEvidenceCodeConverter
- GOGroupValueObject
- GoldenPath
- GoldenPathQuery
- GoldenPathSequenceAnalysis
- GoMetric
- GoMetric.Metric
- GoMetricImpl
- GoogleAnalytics4Provider
- GoTerm2GeneEndpoint
- GroupAuthority
- GroupAuthority.Factory
- GroupAuthorityImpl
- GwasDatabaseImporterCli
- GZIP
- GzipHeaderDecorator
- H2Dialect
- Hibernate4Metrics
- Hibernate4QueryMetrics
- HibernateMonitor
- HibernateMonitorImpl
- HibernateSearchException
- HibernateSearchSource
- HibernateUtils
- Highlighter
- HikariCPMetrics
- HitListSize
- HitListSize.Factory
- HomePageController
- HomologeneFetcher
- HomologeneService
- HomologeneServiceFactory
- HomologeneServiceImpl
- HttpArchiveFetcherInterface
- HttpFetcher
- HumanCoexpressionSupportDetailsImpl
- HumanExperimentCoexpressionLinkImpl
- HumanGeneCoExpression
- HumanGeneCoExpression.Factory
- HumanGeneCoExpressionImpl
- IdArray
- IdArrayValueObject
- Identifiable
- IdentifiableValueObject
- IgnoreAudit
- IlluminaProbeReader
- Image
- ImageSeries
- IncludedResultSetInfoValueObject
- IndexController
- IndexerService
- IndexerServiceImpl
- IndexerTask
- IndexerTaskCommand
- IndexerTaskImpl
- IndexGemmaCLI
- InferredQuantitationMismatchException
- InsufficientDataException
- InsufficientProbesException
- InsufficientSamplesException
- Investigation
- IOExceptionWithRetry
- JacksonConfig
- JavascriptLogger
- JobInfo
- JobInfo.Factory
- JsonFileService
- JsonMappingExceptionMapper
- JsonReaderResponse
- JSONTableRenderer
- JsonUtil
- JSONView
- Keyword
- Keyword.Factory
- LabelValue
- LimitArg
- LimitedResponseDataObject
- LinearModelAnalyzer
- LineMapParser
- LineParser
- LinkAnalysis
- LinkAnalysisCli
- LinkAnalysisConfig
- LinkAnalysisConfig.NormalizationMethod
- LinkAnalysisConfig.SingularThreshold
- LinkAnalysisController
- LinkAnalysisEvent
- LinkAnalysisPersister
- LinkAnalysisPersisterImpl
- LinkAnalysisService
- LinkAnalysisServiceImpl
- LinkAnalysisTaskCommand
- LinkAnalysisTaskImpl
- LinkCreator
- ListBatchCommand
- ListUtils
- LiteratureEvidence
- LiteratureEvidence.Factory
- LiteratureEvidenceDao
- LiteratureEvidenceDaoImpl
- LiteratureEvidenceValueObject
- LoadEvidenceForClassifier
- LoadExpressionDataCli
- LoadSimpleExpressionDataCli
- LocalDatasetFetcher
- LocalFile
- LocalFile.Factory
- LocalSeriesFetcher
- Log4jConfigurer
- LoggingConfigurer
- LuceneHighlighter
- LuceneParseSearchException
- LuceneQueryUtils
- MailEngine
- MailEngineImpl
- MailUtils
- MailUtilsImpl
- MaintenanceModeController
- MakeExperimentPrivateCli
- MakeExperimentsPublicCli
- MakePrivateEvent
- MakePublicEvent
- MalformedArgException
- MalformedArgExceptionMapper
- ManualAnnotationEvent
- MatrixRowPairAnalysis
- MatrixWriter
- MeanVarianceRelation
- MeanVarianceRelation.Factory
- MeanVarianceService
- MeanVarianceServiceHelper
- MeanVarianceServiceImpl
- MeanVarianceUpdateEvent
- Measurement
- Measurement.Factory
- MeasurementKind
- MeasurementType
- MeasurementValueObject
- MediaTypeUtils
- MedicalSubjectHeading
- MedicalSubjectHeading.Factory
- MeshTermFetcherCli
- MessageUtil
- MessageUtilImpl
- MetaFile
- MeterRegistryCliConfigurer
- MeterRegistryEhcacheConfigurer
- MeterRegistryWebConfigurer
- MetricsApplicationEventListener
- MinifierPostProcessor
- MissingResult
- MissingValueAnalysisEvent
- MondoOntologyService
- MonitoredDiskFileItem
- MonitoredDiskFileItemFactory
- MonitoredOutputStream
- MouseCoexpressionSupportDetailsImpl
- MouseExperimentCoexpressionLinkImpl
- MouseGeneCoExpression
- MouseGeneCoExpression.Factory
- MouseGeneCoExpressionImpl
- Multifunctionality
- Multifunctionality.Factory
- MultifunctionalityCli
- MySQL57InnoDBDialect
- NCBIGene2Accession
- NcbiGene2AccessionParser
- NCBIGene2GOAssociationLoader
- NCBIGene2GOAssociationLoaderCLI
- NCBIGene2GOAssociationParser
- NcbiGeneConverter
- NcbiGeneData
- NcbiGeneDomainObjectGenerator
- NcbiGeneEnsemblFileParser
- NCBIGeneFileFetcher
- NcbiGeneHistory
- NcbiGeneHistoryParser
- NCBIGeneInfo
- NCBIGeneInfo.GeneType
- NCBIGeneInfo.NomenclatureStatus
- NcbiGeneInfoParser
- NcbiGeneLoader
- NcbiGeneLoaderCLI
- NCBIUtil
- NeedsAttentionEvent
- NetDatasourceUtil
- NewsItem
- NonPersistentNonOrderedCoexpLink
- NonRetainedResult
- NoRowsLeftAfterFilteringException
- NotFoundExceptionMapper
- NotTroubledStatusFlagEvent
- ObjectMapperResolver
- OffsetArg
- OmimDatabaseImporterCli
- OntologyController
- OntologyHighlighter
- OntologyIndividualSimple
- OntologyPropertySimple
- OntologySearchSource
- OntologyService
- OntologyServiceFactory
- OntologyServiceImpl
- OntologyUtils
- OpenApiUtils
- OrderVectorsByDesignCli
- OtherCoexpressionSupportDetailsImpl
- OtherExperimentCoexpressionLinkImpl
- OtherGeneCoExpression
- OtherGeneCoExpression.Factory
- OtherGeneCoExpressionImpl
- OutlierAnalysisEvent
- OutlierDetails
- OutlierDetectionService
- OutlierDetectionServiceImpl
- OutlierFlaggingService
- OutlierFlaggingServiceImpl
- OutlierFoundAnalysisEvent
- OutliersNotFoundAnalysisEvent
- OutputStreamListener
- PaginatedResponseDataObject
- Parser
- ParserAndLoaderTools
- ParseSearchException
- ParsingStreamConsumer
- PatoOntologyService
- PCAAnalysisEvent
- PearsonMetrics
- PermissionChangeEvent
- Persister
- PersisterHelper
- PersisterHelperImpl
- Person
- PersonDao
- PersonDaoImpl
- PhenotypeAssociation
- PhenotypeAssociationConstants
- PhenotypeAssociationDao
- PhenotypeAssociationDaoImpl
- PhenotypeAssociationManagerService
- PhenotypeAssociationManagerServiceImpl
- PhenotypeAssociationPublication
- PhenotypeAssociationPublication.Factory
- PhenotypeAssociationService
- PhenotypeAssociationServiceImpl
- PhenotypeAssoManagerServiceHelper
- PhenotypeAssoManagerServiceHelperImpl
- PhenotypeAssoOntologyHelper
- PhenotypeAssoOntologyHelperImpl
- PhenotypeAssPubValueObject
- PhenotypeController
- PhenotypeGroupValueObject
- PhenotypeMappingType
- PhenotypeValueObject
- PhenotypeWebService
- PhysicalLocation
- PhysicalLocation.Factory
- PhysicalLocationValueObject
- PlatformArg
- PlatformArgService
- PlatformArrayArg
- PlatformFetcher
- PlatformIdArg
- PlatformStringArg
- PlatformsWebService
- Pointcuts
- PolymerType
- PreparedCoexMatrices
- PreprocessController
- PreprocessExperimentTask
- PreprocessingException
- PreprocessorService
- PreprocessorServiceImpl
- PreprocessTaskCommand
- PreprocessTaskImpl
- PrimitiveType
- PrincipalComponentAnalysis
- PrincipalComponentAnalysis.Factory
- PrincipalComponentAnalysisDao
- PrincipalComponentAnalysisDaoImpl
- PrincipalComponentAnalysisService
- PrincipalComponentAnalysisServiceImpl
- Probe2GeneEndpoint
- ProbeLoading
- ProbeLoading.Factory
- ProbeMapper
- ProbeMapperConfig
- ProbeMapperImpl
- ProbeMapUtils
- ProbeSequenceParser
- ProcessedDataComputeCLI
- ProcessedDataVectorCache
- ProcessedDataVectorCacheImpl
- ProcessedExpressionDataVector
- ProcessedExpressionDataVector.Factory
- ProcessedExpressionDataVectorDao
- ProcessedExpressionDataVectorDao.RankMethod
- ProcessedExpressionDataVectorDaoImpl
- ProcessedExpressionDataVectorService
- ProcessedExpressionDataVectorServiceImpl
- ProcessedVectorComputationEvent
- ProgressData
- ProgressStatusService
- ProgressStatusServiceImpl
- ProgressUpdateAppender
- ProgressUpdateAppender.ProgressUpdateCallback
- ProgressUpdateAppender.ProgressUpdateContext
- PropertyMapping
- PropertyMappingUtils
- Protocol
- Protocol.Factory
- ProtocolDao
- ProtocolDaoImpl
- ProtocolService
- ProtocolServiceImpl
- PubMedLoaderCli
- PubMedQueryController
- PubMedQueryControllerImpl
- PubMedSearch
- PubMedSearchCommand
- PubMedSearcher
- PubMedService
- PubMedXMLFetcher
- PubMedXMLParser
- PvalueDistribution
- PvalueDistribution.Factory
- QuantileNormalizer
- QuantitationMismatchException
- QuantitationMismatchPreprocessingException
- QuantitationType
- QuantitationType.Factory
- QuantitationTypeArg
- QuantitationTypeArgService
- QuantitationTypeByIdArg
- QuantitationTypeByNameArg
- QuantitationTypeConversionException
- QuantitationTypeDao
- QuantitationTypeDaoImpl
- QuantitationTypeParameterGuesser
- QuantitationTypePropertyEditor
- QuantitationTypeService
- QuantitationTypeServiceImpl
- QuantitationTypeValueObject
- QueriedAndFilteredAndPaginatedResponseDataObject
- QueriedAndFilteredResponseDataObject
- QueryArg
- QueryUtils
- QueuingParser
- RankComputationEvent
- RatCoexpressionSupportDetailsImpl
- RatExperimentCoexpressionLinkImpl
- RatGeneCoExpression
- RatGeneCoExpression.Factory
- RatGeneCoExpressionImpl
- RawAndProcessedExpressionDataVectorDao
- RawAndProcessedExpressionDataVectorDaoImpl
- RawAndProcessedExpressionDataVectorService
- RawAndProcessedExpressionDataVectorServiceImpl
- RawDataFetcher
- RawExpressionDataVector
- RawExpressionDataVector.Factory
- RawExpressionDataVectorDao
- RawExpressionDataVectorDaoImpl
- RawExpressionDataVectorService
- RawExpressionDataVectorServiceImpl
- ReCaptcha
- ReCaptchaException
- ReCaptchaResponse
- RecordParser
- ReferenceAssociation
- ReferenceAssociation.Factory
- ReferenceAssociationDao
- ReferenceAssociationDaoImpl
- RelationshipPersister
- ReleaseDetailsUpdateEvent
- RepeatScan
- ReplaceDataCli
- Reporter
- Reporter.Factory
- RequestAttributesBasedClientIdRetrievalStrategy
- RequestExceptionEventListener
- RequestExceptionLogger
- RequestHeaderBasedClientIdRetrievalStrategy
- RequestUtil
- ResetSuitabilityForDifferentialExpressionAnalysisEvent
- Responder
- Responder.FilterMethod
- ResponseDataObject
- ResponseErrorObject
- RestapidocsIndexRewriteFilter
- RestAuthEntryPoint
- Retryable
- RetryLogger
- RgdDatabaseImporterCli
- RNASeqBatchInfoCli
- RNASeqDataAddCli
- RootWebService
- RootWebService.ApiInfoValueObject
- RootWebService.UserValueObject
- RowLevelFilter
- RowLevelFilter.Method
- RowMissingValueFilter
- RowsWithSequencesFilter
- RssFeedController
- SampleCoexpressionAnalysis
- SampleCoexpressionAnalysisService
- SampleCoexpressionAnalysisServiceImpl
- SampleCoexpressionMatrix
- SampleCoexpressionRelatedPreprocessingException
- SampleCorrelationAnalysisEvent
- SampleRemovalEvent
- SampleRemovalReversionEvent
- ScaleType
- ScaleTypeConverter
- ScanDateExtractor
- ScoreValueObject
- SDRFFetcher
- SearchException
- SearchResult
- SearchResultDisplayObject
- SearchResultSet
- SearchService
- SearchService.SearchResultMap
- SearchServiceImpl
- SearchSettings
- SearchSettings.SearchMode
- SearchSettingsValueObject
- SearchSource
- SearchWebService
- SearchWebService.SearchResultsResponseDataObject
- SearchWebService.SearchResultValueObject
- SecureMethodInvokingJobDetailFactoryBean
- SecurityController
- SecurityControllerImpl
- SecurityInfoValueObject
- SequenceBinUtils
- SequenceManipulation
- SequenceSimilaritySearchResult
- SequenceType
- SequenceTypePropertyEditor
- SequenceTypeValueObject
- SequenceWriter
- SeriesFetcher
- ServiceBasedEntityConverter
- ServiceBasedValueObjectConverter
- ServiceUnavailableException
- ServletMetricsFilter
- ServletUtils
- SessionBoundExpressionExperimentSetValueObject
- SessionBoundGeneSetValueObject
- SessionListManager
- SessionListManagerImpl
- Settings
- SettingsConfig
- SfariDatabaseImporterCli
- SFARIIntermediateFileParser
- SFARILineInfo
- ShellDelegatingBlat
- ShellDelegatingBlat.BlattableGenome
- ShortBibliographicReferenceTag
- SidValueObject
- SignupController
- SimpleExpressionDataLoaderService
- SimpleExpressionDataLoaderServiceImpl
- SimpleExpressionExperimentCommandValidation
- SimpleExpressionExperimentLoadTaskCommand
- SimpleExpressionExperimentMetaData
- SimpleFastaCmd
- SimpleHTMLFormatter
- SimpleHttp
- SimpleMarkdownFormatter
- SimplePageContext
- SimpleTreeValueObject
- SingleBatchDeterminationEvent
- SingleExperimentAnalysis
- SingleExperimentAnalysisDao
- SingleExperimentAnalysisDaoBase
- SingleExperimentAnalysisService
- SingletonBatchesException
- SingletonBatchInvalidEvent
- SlackAppender
- Slice
- Sort
- Sort.Direction
- SortArg
- SortArg.Sort
- SortArg.Sort.Direction
- SortValueObject
- SourceDomainObjectGenerator
- SpearmanMetrics
- SplitExperimentCli
- SplitExperimentService
- SplitExperimentServiceImpl
- SpringContextUtil
- StandardQuantitationType
- StandardQuantitationTypeConverter
- StartupListener
- Statement
- Statement.Factory
- StatementDao
- StatementDaoImpl
- StatementValueObject
- StopWatchUtils
- StopWatchUtils.StopWatchRegion
- StringArrayArg
- StringPoint
- SubmittedTask
- SubmittedTask.Status
- SubmittedTaskAbstract
- SubmittedTaskLocal
- SubmittedTasksMaintenance
- SubmittedTaskValueObject
- Subquery
- Subquery.Alias
- SubqueryUtils
- SupportDetails
- SuspiciousValuesForQuantitationException
- SuspiciousValuesForQuantitationException.SuspiciousValueResult
- SVDCli
- SvdController
- SVDException
- SVDRelatedPreprocessingException
- SVDService
- SVDServiceHelper
- SVDServiceHelperImpl
- SVDServiceImpl
- SvdTask
- SvdTaskCommand
- SvdTaskImpl
- SVDValueObject
- SwissProtParser
- SystemMonitorController
- SystemStatsController
- TableMaintenanceUtil
- TableMaintenanceUtilImpl
- Task
- TaskCancelledException
- TaskCommand
- TaskCommandToTaskMatcher
- TaskCommandToTaskMatcherImpl
- TaskCompletionController
- TaskPostProcessing
- TaskPostProcessingImpl
- TaskResult
- TaskRunningService
- TaskRunningServiceImpl
- TaxaWebService
- Taxon
- Taxon.Factory
- TaxonArg
- TaxonArgService
- TaxonArrayArg
- TaxonDao
- TaxonDaoImpl
- TaxonFetcher
- TaxonIdArg
- TaxonLoader
- TaxonLoaderCli
- TaxonNameArg
- TaxonNcbiIdArg
- TaxonParser
- TaxonPropertyEditor
- TaxonService
- TaxonServiceImpl
- TaxonUtility
- TaxonValueObject
- TechnologyType
- TestComponent
- TextView
- TGFVO
- ThreadPoolTaskExecutorMetrics
- ThreePrimeDistanceMethod
- TimeUtil
- TooSmallDatasetLinkAnalysisEvent
- Treatment
- Treatment.Factory
- TreeCharacteristicValueObject
- TroubledStatusFlagEvent
- TsvFileService
- TwoChannelMissingValueController
- TwoChannelMissingValueHelperService
- TwoChannelMissingValues
- TwoChannelMissingValuesImpl
- TwoChannelMissingValueTaskCommand
- TwoChannelMissingValueTaskImpl
- TypedResultTransformer
- UnhandledExceptionMapper
- UnhandledExceptionResolver
- UninformativeFASTQHeadersForBatchingEvent
- Unit
- Unit.Factory
- UnitDao
- UnitDaoImpl
- UnsuitableForAnalysisException
- UnsuitableForDifferentialExpressionAnalysisEvent
- UnsupportedQuantitationScaleConversionException
- UnsupportedRawdataFileFormatException
- UpdateEE2CCli
- UpdateEEDetailsCommand
- UpdatePubMedCli
- UpdatePubMedCommand
- UploadInfo
- UploadListener
- User
- User.Factory
- UserCounterListener
- UserDao
- UserDaoImpl
- UserFormMultiActionController
- UserGroup
- UserGroup.Factory
- UserGroupDao
- UserGroupDaoImpl
- UserGroupValueObject
- UserIdRetrievalStrategy
- UserListController
- UserListControllerImpl
- UserManager
- UserManagerImpl
- UserQuery
- UserQuery.Factory
- UserService
- UserServiceImpl
- UserTracker
- UserUpdateCommand
- UserValueObject
- ValidateEvidenceValueObject
- ValueObject
- ValueObjectConfig
- VectorMergingCli
- VectorMergingService
- VectorMergingServiceImpl
- Versioned
- VersionedEvent
- VisualizationValueObject
- WebApplicationExceptionMapper
- WebConstants
- WellComposedErrorBody
- WhatsNew
- WhatsNewController
- WhatsNewService
- WhatsNewServiceImpl
- XMLUtils
- XmlView