All Classes
AbaGene
ABALinkOutValueObject
AbstractAnalyzer
AbstractArg
AbstractArrayArg
AbstractAuditable
AbstractCLI
AbstractCLIContextCLI
AbstractCriteriaFilteringVoEnabledDao
AbstractCuratableDao
AbstractCuratableValueObject
AbstractDao
AbstractDescribable
AbstractDesignElementDataVectorService
AbstractDifferentialExpressionAnalyzer
AbstractEntityArg
AbstractEntityArrayArg
AbstractExceptionMapper
AbstractFetcher
AbstractFilteringVoEnabledDao
AbstractFilteringVoEnabledService
AbstractFilteringVoEnabledService.ObjectFilterPropertyMeta
AbstractGemmaEndpoint
AbstractGeoService
AbstractMatrixRowPairAnalysis
AbstractPersister
AbstractPersister.Caches
AbstractQueryFilteringVoEnabledDao
AbstractQueryFilteringVoEnabledDao.QueryHint
AbstractService
AbstractSetListContainer
AbstractSpringAwareCLI
AbstractTask
AbstractTsvFileService
AbstractVoEnabledDao
AbstractVoEnabledService
AccessDeniedExceptionMapper
AclAdvice
AclAfterCollectionCompSeqByArrayDesignFilter
AclAfterCollectionDataVectorByExpressionExperimentFilter
AclCriteriaUtils
AclQueryUtils
AffyChipTypeExtractor
AffyDataFromCelCli
AffyPowerToolsProbesetSummarize
AffyProbeCollapseCli
AffyProbeNameFilter
AffyProbeNameFilter.Pattern
AffyProbeReader
AffyScanDateExtractor
AgilentScanDateExtractor
AlignmentBasedGeneMappingEvent
AllenBrainAtlasService
AllenBrainAtlasServiceImpl
AlreadyExistsInSystemException
AlternateName
AlternateName.Factory
AlternateNameImpl
Analysis
AnalysisDao
AnalysisDaoBase
AnalysisResult
AnalysisResultSet
AnalysisResultSetDao
AnalysisResultSetService
AnalysisResultSetsWebService
AnalysisResultSetValueObject
AnalysisResultValueObject
AnalysisSelectionAndExecutionService
AnalysisSelectionAndExecutionServiceImpl
AnalysisService
AnalysisSuitabilityEvent
AnalysisUtilService
AnalysisUtilServiceImpl
AnalysisValueObject
AnchorTagUtil
AnnotationAssociation
AnnotationAssociation.Factory
AnnotationAssociationDao
AnnotationAssociationDaoImpl
AnnotationAssociationService
AnnotationAssociationServiceImpl
AnnotationBasedGeneMappingEvent
AnnotationController
AnnotationEvent
AnnotationsWebService
AnnotationValueObject
ApplicationEventListener
ArchiveFetcher
Arg
ArgModelResolver
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
Auditable
AuditableObject
AuditableUtil
AuditableUtilImpl
AuditAction
AuditAdvice
AuditController
AuditEvent
AuditEvent.Factory
AuditEventDao
AuditEventDaoImpl
AuditEventService
AuditEventServiceImpl
AuditEventType
AuditEventValueObject
AuditHelper
AuditTrail
AuditTrail.Factory
AuditTrailDao
AuditTrailDaoImpl
AuditTrailImpl
AuditTrailService
AuditTrailServiceImpl
AuthenticationExceptionMapper
AutomatedAnnotationEvent
BaseCodeOntologySearchException
BaseController
BaseDao
BaseExpressionDataMatrix
BaseFormController
BaselineSelection
BaseScanDateExtractor
BaseService
BaseValueObject
BaseVoEnabledDao
BaseVoEnabledService
BasicLineMapParser
BasicLineParser
BatchConfound
BatchConfoundUtils
BatchCorrectionEvent
BatchEffectDetails
BatchEffectPopulationCli
BatchInfoFetchController
BatchInfoFetchTask
BatchInfoFetchTaskCommand
BatchInfoFetchTaskImpl
BatchInfoParser
BatchInfoPopulationException
BatchInfoPopulationHelperService
BatchInfoPopulationHelperServiceImpl
BatchInfoPopulationService
BatchInfoPopulationServiceImpl
BatchInformationFetchingEvent
BatchProblemsUpdateEvent
BeanInitializationTimeMonitor
BeanNameGenerator
BibliographicPhenotypesValueObject
BibliographicReference
BibliographicReference.Factory
BibliographicReferenceController
BibliographicReferenceControllerImpl
BibliographicReferenceDao
BibliographicReferenceDaoImpl
BibliographicReferenceService
BibliographicReferenceServiceImpl
BibliographicReferenceValueObject
BibRefAnnotation
BibRefAnnotationImpl
BibRefUpdaterCli
BioAssay
BioAssay.Factory
BioAssayController
BioAssayDao
BioAssayDaoImpl
BioAssayDimension
BioAssayDimension.Factory
BioAssayDimensionDao
BioAssayDimensionDaoImpl
BioAssayDimensionService
BioAssayDimensionServiceImpl
BioAssayDimensionValueObject
BioAssayOutlierProcessingTask
BioAssayOutlierProcessingTaskCommand
BioAssayOutlierProcessingTaskImpl
BioAssayService
BioAssayServiceImpl
BioAssaySet
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
BoolArg
BooleanVectorValueObject
BrowsingDao
BusinessKey
CacheMonitor
CacheMonitorImpl
CacheUtils
ChannelUtils
Characteristic
Characteristic.Factory
CharacteristicBasicValueObject
CharacteristicBrowserController
CharacteristicConverter
CharacteristicDao
CharacteristicDao.CharacteristicByValueUriOrValueCount
CharacteristicDaoImpl
CharacteristicService
CharacteristicServiceImpl
CharacteristicUpdateCommand
CharacteristicUpdateTask
CharacteristicUpdateTaskImpl
CharacteristicValueObject
Chromosome
ChromosomeDao
ChromosomeDaoImpl
ChromosomeFeature
ChromosomeLocation
ChromosomeService
ChromosomeServiceImpl
ChromosomeUtil
CitationValueObject
ClassConverter
CLI
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
CommonsConfigurationPropertyPlaceholderConfigurer
CommonsMultipartFile
CommonsMultipartMonitoredResolver
CompassSearchException
CompassSearchSource
CompassUtils
CompositeSequence
CompositeSequence.Factory
CompositeSequenceArg
CompositeSequenceArrayArg
CompositeSequenceController
CompositeSequenceDao
CompositeSequenceDaoImpl
CompositeSequenceGeneMapperService
CompositeSequenceIdArg
CompositeSequenceMapSummary
CompositeSequenceMapValueObject
CompositeSequenceNameArg
CompositeSequenceParser
CompositeSequenceService
CompositeSequenceServiceImpl
CompositeSequenceValueObject
Compound
Compound.Factory
CompoundDao
CompoundDaoImpl
CompoundService
CompoundServiceImpl
ConfigurationCookie
Constants
ConstantsTag
ConstantsTei
Contact
Contact.Factory
ContactDao
ContactDaoImpl
ContactService
ContactServiceImpl
ContrastResult
ContrastResult.Factory
ContrastResultValueObject
ContrastsValueObject
ContrastVO
ControllerUtils
Converter
CorsFilter
CountObsoleteTermsCli
CtdDatabaseImporterCli
Curatable
CuratableDao
CurationDetails
CurationDetailsDao
CurationDetailsDaoImpl
CurationDetailsEvent
CurationDetailsService
CurationDetailsServiceImpl
CurationNoteUpdateEvent
CustomModelConverter
CustomModelConvertersRegistrationListener
CustomRssViewer
DataAddedEvent
DataAnalysisEvidence
DatabaseBackedGeneSetValueObject
DatabaseEntry
DatabaseEntry.Factory
DatabaseEntryArg
DatabaseEntryArrayArg
DatabaseEntryDao
DatabaseEntryDaoImpl
DatabaseEntryIdArg
DatabaseEntryService
DatabaseEntryServiceImpl
DatabaseEntryStringArg
DatabaseEntryTag
DatabaseEntryValueObject
DatabaseSearchSource
DatabaseSearchSourceUtils
DatabaseType
DatabaseViewGenerator
DatabaseViewGeneratorCLI
DatabaseViewGeneratorImpl
DataFileFetcher
DataReplacedEvent
DatasetArg
DatasetArrayArg
DatasetCombiner
DatasetFetcher
DatasetIdArg
DatasetStringArg
DatasetsWebService
DataUpdater
DataVector
DataVectorValueObject
DEDVController
DEDVfromEEIDGeneIDEndpoint
DEDVRankEndpoint
DeleteDiffExCli
DeleteEvidenceCLI
DeleteExperimentsCli
Describable
DescribableComparator
DesignElementDataVector
DesignElementDataVectorDao
DesignElementDataVectorDaoImpl
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
DifferentialExpressionEvidenceImpl
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
DoubleArg
DoublePointConverter
DoubleVectorValueObject
DummyMailSender
DumpsValueObject
Eigenvalue
Eigenvalue.Factory
Eigenvector
Eigenvector.Factory
EmailNotificationContext
EmptyController
EmptyExpressionMatrix
Ensembl2NcbiValueObject
EntityDelegator
EntityNotFoundException
EntityNotFoundException
EntityNotFoundExceptionMapper
EntityUtils
ESearchXMLParser
EutilFetch
EutilFetch.Mode
EvidenceFilter
EvidenceImporterAbstractCLI
EvidenceImporterCLI
EvidenceSecurityValueObject
EvidenceSourceValueObject
EvidenceValueObject
ExceptionMapperUtils
ExceptionTag
ExecutingTask
ExecutingTask.TaskLifecycleHandler
ExperimentalDesign
ExperimentalDesign.Factory
ExperimentalDesignController
ExperimentalDesignControllerImpl
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
ExperimentAnnotationEndpoint
ExperimentCoexpressionLink
ExperimentDEDVEndpoint
ExperimentExpressionLevelsValueObject
ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject
ExperimentExpressionLevelsValueObject.VectorElementValueObject
ExperimentIDbyTaxonEndpoint
ExperimentIdEndpoint
ExperimentNameEndpoint
ExperimentNumSamplesEndpoint
ExperimentPlatformSwitchHelperService
ExperimentPlatformSwitchHelperServiceImpl
ExperimentQCTag
ExperimentSetListContainer
ExpLevelConsolidationArg
ExpressionAnalysis
ExpressionAnalysisResultSet
ExpressionAnalysisResultSet.Factory
ExpressionAnalysisResultSetArg
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
ExpressionExperimentPlatformSwitchCli
ExpressionExperimentPlatformSwitchEvent
ExpressionExperimentPlatformSwitchService
ExpressionExperimentPrePersistService
ExpressionExperimentPrePersistServiceImpl
ExpressionExperimentPrimaryPubCli
ExpressionExperimentQCController
ExpressionExperimentQCUtils
ExpressionExperimentReportGenerationController
ExpressionExperimentReportService
ExpressionExperimentReportServiceImpl
ExpressionExperimentReportTask
ExpressionExperimentReportTaskCommand
ExpressionExperimentReportTaskImpl
ExpressionExperimentSearchService
ExpressionExperimentSearchServiceImpl
ExpressionExperimentService
ExpressionExperimentServiceImpl
ExpressionExperimentSet
ExpressionExperimentSet.Factory
ExpressionExperimentSetController
ExpressionExperimentSetDao
ExpressionExperimentSetDaoImpl
ExpressionExperimentSetIDsEndpoint
ExpressionExperimentSetService
ExpressionExperimentSetServiceImpl
ExpressionExperimentSetValueObject
ExpressionExperimentSetValueObjectHelper
ExpressionExperimentSetValueObjectHelperImpl
ExpressionExperimentSubSet
ExpressionExperimentSubSet.Factory
ExpressionExperimentSubSetDao
ExpressionExperimentSubSetDaoImpl
ExpressionExperimentSubSetService
ExpressionExperimentSubSetServiceImpl
ExpressionExperimentSubsetValueObject
ExpressionExperimentUploadResponse
ExpressionExperimentValueObject
ExpressionExperimentVectorManipulatingService
ExpressionExperimentVectorMergeEvent
ExpressionExperimentVisualizationCommand
ExpressionPersister
ExpressionProfileDataObject
ExternalDatabase
ExternalDatabase.Factory
ExternalDatabaseAdderCli
ExternalDatabaseDao
ExternalDatabaseDaoImpl
ExternalDatabaseEvidenceImporterAbstractCLI
ExternalDatabases
ExternalDatabaseService
ExternalDatabaseServiceImpl
ExternalDatabaseStatisticsValueObject
ExternalDatabaseUpdaterCli
ExternalDatabaseUtils
ExternalDatabaseValueObject
ExternalFileGeneLoaderCLI
ExternalFileGeneLoaderService
ExternalFileGeneLoaderServiceImpl
FactorAssociatedAnalysisResultSet
FactorProfile
FactorType
FactorValue
FactorValue.Factory
FactorValueArg
FactorValueArrayArg
FactorValueBasicValueObject
FactorValueComparator
FactorValueDao
FactorValueDaoImpl
FactorValueDeletion
FactorValueDeletionImpl
FactorValueIdArg
FactorValueService
FactorValueServiceImpl
FactorValueValueArg
FactorValueValueObject
FactorValueVector
FailedBatchInformationFetchingEvent
FailedBatchInformationMissingEvent
FailedDataReplacedEvent
FailedDifferentialExpressionAnalysisEvent
FailedLinkAnalysisEvent
FailedMissingValueAnalysisEvent
FailedMultipartHttpServletRequest
FailedPCAAnalysisEvent
FailedProcessedVectorComputationEvent
FastaCmd
FastaParser
FASTQHeadersPresentButNotUsableException
FeedReader
Fetcher
FileFormatException
FileUpload
FileUploadController
FileUploadUtil
FilterArg
FilterArg.Filter
FilterArgParseException
FilterConfig
FilteringDao
FilteringException
FilteringService
FilteringVoEnabledDao
FilteringVoEnabledService
Filters
FiltersUtils
FreeTextExpressionExperimentResultsValueObject
FreeTextGeneResultsValueObject
FtpArchiveFetcher
FtpFetcher
Geeq
GeeqAdminValueObject
GeeqCli
GeeqDao
GeeqDaoImpl
GeeqEvent
GeeqService
GeeqServiceImpl
GeeqValueObject
GemmaClassicHomePageController
GemmaCLI
GemmaCLI.CommandGroup
GemmaOntologyService
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
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
GeneralSearchControllerImpl
GeneralType
GenericEvidence
GenericEvidence.Factory
GenericEvidenceDao
GenericEvidenceDaoImpl
GenericEvidenceValueObject
GenericExperiment
GenericExperiment.Factory
GenericExperimentDao
GenericExperimentDaoImpl
GenericGenelistDesignGenerator
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
GOEvidenceCode
GOEvidenceCodeConverter
GOGroupValueObject
GoldenPath
GoldenPathQuery
GoldenPathSequenceAnalysis
GoMetric
GoMetric.Metric
GoTerm2GeneEndpoint
GroupAuthority
GroupAuthority.Factory
GroupAuthorityImpl
GwasDatabaseImporterCli
GZIP
GzipWriterInterceptor
HibernateByteBlobType
HibernateMonitor
HibernateMonitorImpl
HitListSize
HitListSize.Factory
HitListSizeImpl
HomePageController
HomologeneFetcher
HomologeneService
HomologeneServiceImpl
HttpArchiveFetcherInterface
HttpFetcher
HumanCoexpressionSupportDetailsImpl
HumanExperimentCoexpressionLinkImpl
HumanGeneCoExpression
HumanGeneCoExpression.Factory
HumanGeneCoExpressionImpl
IdArray
IdArrayValueObject
Identifiable
IdentifiableValueObject
IlluminaProbeReader
Image
ImageSeries
IncludedResultSetInfoValueObject
IndexController
IndexerResult
IndexerTask
IndexerTaskCommand
IndexerTaskImpl
IndexGemmaCLI
IndexService
IndexServiceImpl
InsufficientDataException
InsufficientProbesException
InsufficientSamplesException
IntArg
Investigation
JacksonConfig
JavascriptLogger
JobInfo
JobInfo.Factory
JsonMappingExceptionMapper
JsonReaderResponse
JSONTableRenderer
JsonUtil
JSONView
Keyword
Keyword.Factory
LabelValue
LimitArg
LinearModelAnalyzer
LineMapParser
LineParser
LinkAnalysis
LinkAnalysisCli
LinkAnalysisConfig
LinkAnalysisConfig.NormalizationMethod
LinkAnalysisConfig.SingularThreshold
LinkAnalysisController
LinkAnalysisEvent
LinkAnalysisPersister
LinkAnalysisPersisterImpl
LinkAnalysisService
LinkAnalysisServiceImpl
LinkAnalysisTaskCommand
LinkAnalysisTaskImpl
LinkCreator
LinkUtils
ListBatchCommand
ListUtils
LiteratureEvidence
LiteratureEvidence.Factory
LiteratureEvidenceDao
LiteratureEvidenceDaoImpl
LiteratureEvidenceValueObject
LoadEvidenceForClassifier
LoadExpressionDataCli
LoadSimpleExpressionDataCli
LocalDatasetFetcher
LocalFile
LocalFile.Factory
LocalSeriesFetcher
LongArg
MailEngine
MailEngineImpl
MailUtils
MailUtilsImpl
MaintenanceModeController
MakeExperimentsPublicCli
MakePrivateEvent
MakePublicEvent
MalformedArgException
MalformedArgExceptionMapper
ManualAnnotationEvent
MatrixRowPairAnalysis
MatrixWriter
MeanVarianceRelation
MeanVarianceRelation.Factory
MeanVarianceService
MeanVarianceServiceHelper
MeanVarianceServiceHelperImpl
MeanVarianceServiceImpl
Measurement
Measurement.Factory
MeasurementImpl
MeasurementKind
MeasurementType
MeasurementValueObject
MediaTypeUtils
MedicalSubjectHeading
MedicalSubjectHeading.Factory
MeshTermFetcherCli
MessageUtil
MessageUtilImpl
MetaFile
MinifierPostProcessor
MissingResult
MissingValueAnalysisEvent
MonitorAdvice
Monitored
MonitoredDiskFileItem
MonitoredDiskFileItemFactory
MonitoredOutputStream
MouseCoexpressionSupportDetailsImpl
MouseExperimentCoexpressionLinkImpl
MouseGeneCoExpression
MouseGeneCoExpression.Factory
MouseGeneCoExpressionImpl
Multifunctionality
Multifunctionality.Factory
MultifunctionalityCli
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
NoProcessedExpressionDataVectorsException
NoRowsLeftAfterFilteringException
NotFoundExceptionMapper
NotTroubledStatusFlagEvent
ObjectFilter
ObjectFilter.Operator
ObjectFilterCriteriaUtils
ObjectFilterQueryUtils
ObjectMapperResolver
OffsetArg
OmimDatabaseImporterCli
OntologyController
OntologyService
OntologyServiceImpl
OpenApiUtils
OrderVectorsByDesignCli
OtherCoexpressionSupportDetailsImpl
OtherExperimentCoexpressionLinkImpl
OtherGeneCoExpression
OtherGeneCoExpression.Factory
OtherGeneCoExpressionImpl
OutlierAnalysisEvent
OutlierDetails
OutlierDetectionService
OutlierDetectionServiceImpl
OutlierFlaggingService
OutlierFlaggingServiceImpl
OutlierFoundAnalysisEvent
OutliersNotFoundAnalysisEvent
OutputStreamListener
PaginatedResponseDataObject
Parser
ParserAndLoaderTools
ParsingStreamConsumer
PCAAnalysisEvent
PearsonMetrics
PermissionChangeEvent
Persister
PersisterHelper
PersisterHelperImpl
Person
PersonDao
PersonDaoImpl
PhenotypeAssociation
PhenotypeAssociationConstants
PhenotypeAssociationDao
PhenotypeAssociationDaoImpl
PhenotypeAssociationManagerService
PhenotypeAssociationManagerServiceImpl
PhenotypeAssociationPublication
PhenotypeAssociationPublication.Factory
PhenotypeAssociationPublicationImpl
PhenotypeAssociationService
PhenotypeAssociationServiceImpl
PhenotypeAssoManagerServiceHelper
PhenotypeAssoManagerServiceHelperImpl
PhenotypeAssoOntologyHelper
PhenotypeAssoOntologyHelperImpl
PhenotypeAssPubValueObject
PhenotypeController
PhenotypeGroupValueObject
PhenotypeMappingType
PhenotypeValueObject
PhenotypeWebService
PhysicalLocation
PhysicalLocation.Factory
PhysicalLocationValueObject
PlatformArg
PlatformArrayArg
PlatformFetcher
PlatformIdArg
PlatformStringArg
PlatformsWebService
Pointcuts
PolymerType
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
ProcessedExpressionDataVectorCreateHelperService
ProcessedExpressionDataVectorCreateHelperServiceImpl
ProcessedExpressionDataVectorDao
ProcessedExpressionDataVectorDao.RankMethod
ProcessedExpressionDataVectorDaoImpl
ProcessedExpressionDataVectorService
ProcessedExpressionDataVectorServiceImpl
ProcessedVectorComputationEvent
ProgressData
ProgressStatusService
ProgressStatusServiceImpl
ProgressUpdateAppender
ProgressUpdateAppender.ProgressUpdateCallback
ProgressUpdateAppender.ProgressUpdateContext
Protocol
Protocol.Factory
ProtocolDao
ProtocolDaoImpl
ProtocolService
ProtocolServiceImpl
PubMedLoaderCli
PubMedQueryController
PubMedQueryControllerImpl
PubMedSearch
PubMedSearchCommand
PubMedSearcher
PubMedService
PubMedXMLFetcher
PubMedXMLParser
PvalueDistribution
PvalueDistribution.Factory
QuantileNormalizer
QuantitationType
QuantitationType.Factory
QuantitationTypeArg
QuantitationTypeByIdArg
QuantitationTypeByNameArg
QuantitationTypeDao
QuantitationTypeDaoImpl
QuantitationTypeImpl
QuantitationTypeParameterGuesser
QuantitationTypePropertyEditor
QuantitationTypeService
QuantitationTypeServiceImpl
QuantitationTypeValueObject
QueuingParser
RankComputationEvent
RatCoexpressionSupportDetailsImpl
RatExperimentCoexpressionLinkImpl
RatGeneCoExpression
RatGeneCoExpression.Factory
RatGeneCoExpressionImpl
RawDataFetcher
RawExpressionDataVector
RawExpressionDataVector.Factory
RawExpressionDataVectorDao
RawExpressionDataVectorDaoImpl
RawExpressionDataVectorService
RawExpressionDataVectorServiceImpl
ReCaptcha
ReCaptchaException
ReCaptchaResponse
RecordParser
ReferenceAssociation
ReferenceAssociation.Factory
ReferenceAssociationDao
ReferenceAssociationDaoImpl
ReferenceAssociationImpl
RelationshipPersister
ReleaseDetailsUpdateEvent
RepeatScan
ReplaceDataCli
Reporter
Reporter.Factory
RequestExceptionLogger
RequestUtil
ResetSuitabilityForDifferentialExpressionAnalysisEvent
Responder
ResponseDataObject
ResponseErrorObject
RestapidocsIndexRewriteFilter
RestAuthEntryPoint
Retryable
RetryLogger
RgdDatabaseImporterCli
RNASeqBatchInfoCli
RNASeqDataAddCli
RootWebService
RootWebService.ApiInfoValueObject
RowLevelFilter
RowLevelFilter.Method
RowMissingValueFilter
RowsWithSequencesFilter
RssFeedController
SampleCoexpressionAnalysis
SampleCoexpressionAnalysisService
SampleCoexpressionAnalysisServiceImpl
SampleCoexpressionMatrix
SampleRemovalEvent
SampleRemovalReversionEvent
ScaleType
ScaleTypeConverter
ScanDateExtractor
SchedulerUtils
ScoreValueObject
SDRFFetcher
SearchException
SearchResult
SearchResultDisplayObject
SearchResultTypeAllowableValuesModelResolver
SearchService
SearchService.SearchResultMap
SearchServiceImpl
SearchSettings
SearchSettingsValueObject
SearchSource
SearchWebService
SearchWebService.SearchResultsResponseDataObject
SearchWebService.SearchResultValueObject
SecureMethodInvokingJobDetailFactoryBean
SecurityController
SecurityControllerImpl
SecurityInfoValueObject
SequenceBinUtils
SequenceManipulation
SequenceSimilaritySearchResult
SequenceType
SequenceTypePropertyEditor
SequenceTypeValueObject
SequenceWriter
SeriesFetcher
ServletUtils
SessionBoundExpressionExperimentSetValueObject
SessionBoundGeneSetValueObject
SessionListManager
SessionListManagerImpl
Settings
SfariDatabaseImporterCli
SFARIIntermediateFileParser
SFARILineInfo
ShellDelegatingBlat
ShellDelegatingBlat.BlattableGenome
ShortBibliographicReferenceTag
SidValueObject
SignupController
SimpleExpressionDataLoaderService
SimpleExpressionDataLoaderServiceImpl
SimpleExpressionExperimentCommandValidation
SimpleExpressionExperimentLoadTaskCommand
SimpleExpressionExperimentMetaData
SimpleFastaCmd
SimpleHttp
SimpleTreeValueObject
SingleBatchDeterminationEvent
SingleExperimentAnalysis
SingletonBatchesException
SingletonBatchInvalidEvent
SlackAppender
Slice
Sort
Sort.Direction
SortArg
SortArg.Sort
SortArg.Sort.Direction
SortValueObject
SourceDomainObjectGenerator
SpearmanMetrics
SplitExperimentCli
SplitExperimentService
SplitExperimentServiceImpl
SpringContextUtil
StandardQuantitationType
StandardQuantitationTypeConverter
StartupListener
StopWatchUtils
StopWatchUtils.StopWatchRegion
StringArg
StringArrayArg
StringPoint
StringUtils
SubmittedTask
SubmittedTask.Status
SubmittedTaskAbstract
SubmittedTaskLocal
SubmittedTasksMaintenance
SubmittedTaskValueObject
SupportDetails
SVDCli
SvdController
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
TaxonArrayArg
TaxonDao
TaxonDaoImpl
TaxonFetcher
TaxonIdArg
TaxonLoader
TaxonLoaderCli
TaxonNameArg
TaxonNcbiIdArg
TaxonParser
TaxonPropertyEditor
TaxonService
TaxonServiceImpl
TaxonUtility
TaxonValueObject
TechnologyType
TestComponent
TextView
ThreePrimeDistanceMethod
TimeUtil
TooSmallDatasetLinkAnalysisEvent
Treatment
Treatment.Factory
TreeCharacteristicValueObject
TroubledStatusFlagEvent
TsvFileService
TwoChannelMissingValueCLI
TwoChannelMissingValueController
TwoChannelMissingValueHelperService
TwoChannelMissingValueHelperServiceImpl
TwoChannelMissingValues
TwoChannelMissingValuesImpl
TwoChannelMissingValueTaskCommand
TwoChannelMissingValueTaskImpl
UnhandledExceptionMapper
UninformativeFASTQHeadersForBatchingEvent
Unit
Unit.Factory
UnitDao
UnitDaoImpl
UnitImpl
UnknownLogScaleException
UnsuitableForAnalysisException
UnsuitableForDifferentialExpressionAnalysisEvent
UnsupportedRawdataFileFormatException
UpdateEEDetailsCommand
UpdatePubMedCli
UpdatePubMedCommand
UploadInfo
UploadListener
User
User.Factory
UserCounterListener
UserDao
UserDaoImpl
UserFormMultiActionController
UserGroup
UserGroup.Factory
UserGroupDao
UserGroupDaoImpl
UserGroupValueObject
UserListController
UserListControllerImpl
UserManager
UserManagerImpl
UserQuery
UserQuery.Factory
UserService
UserServiceImpl
UserTracker
UserUpdateCommand
UserValueObject
ValidateEvidenceValueObject
ValueObject
VectorMergingCli
VectorMergingHelperService
VectorMergingHelperServiceImpl
VectorMergingService
VectorMergingServiceImpl
Versioned
VersionedEvent
VisualizationValueObject
WebApplicationExceptionMapper
WebConstants
WellComposedErrorBody
WhatsNew
WhatsNewController
WhatsNewService
WhatsNewServiceImpl
XMLUtils
XmlView