Hierarchy For All Packages
Package Hierarchies:Class Hierarchy
- java.lang.Object
- ubic.gemma.cli.util.AbstractCLI (implements org.springframework.context.ApplicationContextAware, ubic.gemma.cli.util.CLI)
- ubic.gemma.cli.util.AbstractAuthenticatedCLI (implements org.springframework.context.EnvironmentAware, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.cli.util.AbstractAutoSeekingCLI<T>
- ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
- ubic.gemma.apps.AffyProbeCollapseCli
- ubic.gemma.apps.ArrayDesignAnnotationFileCli
- ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli
- ubic.gemma.apps.ArrayDesignBioSequenceDetachCli
- ubic.gemma.apps.ArrayDesignBlatCli
- ubic.gemma.apps.ArrayDesignMapSummaryCli
- ubic.gemma.apps.ArrayDesignMergeCli
- ubic.gemma.apps.ArrayDesignProbeCleanupCLI
- ubic.gemma.apps.ArrayDesignProbeMapperCli
- ubic.gemma.apps.ArrayDesignProbeRenamerCli
- ubic.gemma.apps.ArrayDesignRepeatScanCli
- ubic.gemma.apps.ArrayDesignSequenceAssociationCli
- ubic.gemma.apps.ArrayDesignSubsumptionTesterCli
- ubic.gemma.apps.BioSequenceCleanupCli
- ubic.gemma.apps.ExpressionExperimentManipulatingCLI
- ubic.gemma.apps.AffyDataFromCelCli
- ubic.gemma.apps.BatchEffectPopulationCli
- ubic.gemma.apps.DeleteDiffExCli
- ubic.gemma.apps.DeleteExperimentsCli
- ubic.gemma.apps.DetectQuantitationTypeCli
- ubic.gemma.apps.DifferentialExpressionAnalysisCli
- ubic.gemma.apps.ExperimentalDesignImportCli
- ubic.gemma.apps.ExperimentalDesignWriterCLI
- ubic.gemma.apps.ExpressionDataCorrMatCli
- ubic.gemma.apps.ExpressionDataMatrixWriterCLI
- ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli
- ubic.gemma.apps.ExpressionExperimentDataUpdaterCli
- ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli
- ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli
- ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli
- ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli
- ubic.gemma.apps.ExpressionExperimentPrimaryPubCli
- ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli<T>
- ubic.gemma.apps.ListQuantitationTypesCli
- ubic.gemma.apps.ProcessedDataDeleterCli
- ubic.gemma.apps.RawDataDeleterCli
- ubic.gemma.apps.RawExpressionDataWriterCli
- ubic.gemma.apps.SingleCellDataAggregateDeleterCli
- ubic.gemma.apps.SingleCellDataAggregatorCli
- ubic.gemma.apps.SingleCellDataDeleterCli
- ubic.gemma.apps.SingleCellDataWriterCli
- ubic.gemma.apps.GeeqCli
- ubic.gemma.apps.LinkAnalysisCli
- ubic.gemma.apps.LockExpressionDataFileCli
- ubic.gemma.apps.MakeExperimentPrivateCli
- ubic.gemma.apps.MakeExperimentsPublicCli
- ubic.gemma.apps.OrderVectorsByDesignCli
- ubic.gemma.apps.ProcessedDataComputeCLI
- ubic.gemma.apps.RefreshExperimentCli
- ubic.gemma.apps.ReplaceDataCli
- ubic.gemma.apps.RNASeqBatchInfoCli
- ubic.gemma.apps.RNASeqDataAddCli
- ubic.gemma.apps.SingleCellDataLoaderCli
- ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli
- ubic.gemma.apps.SplitExperimentCli
- ubic.gemma.apps.SVDCli
- ubic.gemma.apps.VectorMergingCli
- ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
- ubic.gemma.apps.ArrayDesignAlternativePopulateCli
- ubic.gemma.apps.BibRefUpdaterCli
- ubic.gemma.apps.BlacklistCli
- ubic.gemma.apps.CompleteCli
- ubic.gemma.apps.DatabaseViewGeneratorCLI
- ubic.gemma.apps.ExperimentalDesignViewCli
- ubic.gemma.apps.ExternalDatabaseAdderCli
- ubic.gemma.apps.ExternalDatabaseOverviewCli
- ubic.gemma.apps.ExternalDatabaseUpdaterCli
- ubic.gemma.apps.ExternalFileGeneLoaderCLI
- ubic.gemma.apps.FactorValueMigratorCLI
- ubic.gemma.apps.FindObsoleteTermsCli
- ubic.gemma.apps.FixOntologyTermLabelsCli
- ubic.gemma.apps.GenericGenelistDesignGenerator
- ubic.gemma.apps.GeoGrabberCli (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.apps.LoadExpressionDataCli
- ubic.gemma.apps.LoadSimpleExpressionDataCli
- ubic.gemma.apps.MultifunctionalityCli
- ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI
- ubic.gemma.apps.NcbiGeneLoaderCLI
- ubic.gemma.apps.ProtocolAdderCli
- ubic.gemma.apps.ProtocolDeleterCli
- ubic.gemma.apps.ProtocolListCli
- ubic.gemma.apps.PubMedLoaderCli
- ubic.gemma.apps.PubMedSearcher
- ubic.gemma.apps.TaxonLoaderCli
- ubic.gemma.apps.UpdateEe2AdCli
- ubic.gemma.apps.UpdateEE2CCli
- ubic.gemma.apps.UpdateGene2CsCli
- ubic.gemma.apps.UpdatePubMedCli
- ubic.gemma.cli.util.AbstractAutoSeekingCLI<T>
- ubic.gemma.apps.GenerateDatabaseUpdateCli
- ubic.gemma.apps.IndexGemmaCLI
- ubic.gemma.apps.InitializeDatabaseCli
- ubic.gemma.apps.ListExpressionDataFIleLocksCli
- ubic.gemma.apps.MeshTermFetcherCli
- ubic.gemma.apps.SingleCellDataDownloaderCli
- ubic.gemma.apps.SingleCellDataTransformCli
- ubic.gemma.apps.UnifiedOntologyUpdaterCli
- ubic.gemma.apps.UpdateDatabaseCli
- ubic.gemma.cli.util.AbstractAuthenticatedCLI (implements org.springframework.context.EnvironmentAware, org.springframework.beans.factory.InitializingBean)
- ubic.gemma.cli.completion.AbstractCompletionGenerator (implements ubic.gemma.cli.completion.CompletionGenerator)
- ubic.gemma.cli.completion.BashCompletionGenerator
- ubic.gemma.cli.completion.FishCompletionGenerator
- ubic.gemma.cli.batch.AbstractDelegatingExecutorService (implements java.util.concurrent.ExecutorService)
- ubic.gemma.cli.batch.BatchTaskExecutorService
- ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
- ubic.gemma.cli.metrics.MeterRegistryCliConfigurer (implements org.springframework.context.ApplicationContextAware)
- ubic.gemma.cli.batch.BatchTaskProcessingResult (implements java.io.Serializable)
- ubic.gemma.cli.batch.BatchTaskProgressReporter (implements java.lang.AutoCloseable)
- ubic.gemma.cli.authentication.CLIAuthenticationManager
- ubic.gemma.cli.completion.CompletionSource.Completion
- ubic.gemma.cli.completion.CompletionUtils
- ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter (implements ubic.gemma.cli.batch.BatchTaskSummaryWriter)
- ubic.gemma.cli.config.ConfigurationLinter (implements org.springframework.context.ApplicationListener<E>)
- ubic.gemma.cli.util.EntityLocatorImpl (implements ubic.gemma.cli.util.EntityLocator)
- ubic.gemma.cli.util.EntityOptionsUtils
- ubic.gemma.cli.util.EnumConverter<T> (implements ubic.gemma.cli.util.EnumeratedConverter<T,E>)
- ubic.gemma.cli.util.EnumeratedByCommandStringConverter (implements ubic.gemma.cli.util.EnumeratedByCommandConverter<T,E>)
- ubic.gemma.cli.util.EnumeratedStringConverter (implements ubic.gemma.cli.util.EnumeratedConverter<T,E>)
- ubic.gemma.cli.util.FileUtils
- ubic.gemma.cli.main.GemmaCLI
- ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator (implements ubic.gemma.cli.authentication.CLIAuthenticationAware)
- ubic.gemma.cli.config.GemmaRestApiClientConfig
- ubic.gemma.cli.util.HelpUtils
- ubic.gemma.cli.logging.log4j.Log4jConfigurer (implements ubic.gemma.cli.logging.LoggingConfigurer)
- ubic.gemma.cli.completion.LoggerCompletionSource (implements ubic.gemma.cli.completion.CompletionSource)
- ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter (implements ubic.gemma.cli.batch.BatchTaskSummaryWriter)
- ubic.gemma.cli.util.OptionsUtils
- ubic.gemma.cli.util.PrototypeScopeResolver (implements org.springframework.context.annotation.ScopeMetadataResolver)
- ubic.gemma.cli.completion.SettingsCompletionSource (implements ubic.gemma.cli.completion.CompletionSource)
- ubic.gemma.cli.util.ShellUtils
- ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter (implements ubic.gemma.cli.batch.BatchTaskSummaryWriter)
- ubic.gemma.cli.util.SystemCliContext (implements ubic.gemma.cli.util.CliContext)
- ubic.gemma.cli.batch.TextBatchTaskSummaryWriter (implements ubic.gemma.cli.batch.BatchTaskSummaryWriter)
- ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter (implements ubic.gemma.cli.batch.BatchTaskSummaryWriter)
- ubic.gemma.cli.util.AbstractCLI (implements org.springframework.context.ApplicationContextAware, ubic.gemma.cli.util.CLI)
Interface Hierarchy
- java.lang.AutoCloseable
- java.io.Closeable
- ubic.gemma.cli.batch.BatchTaskSummaryWriter
- java.io.Closeable
- ubic.gemma.cli.util.CLI
- ubic.gemma.cli.authentication.CLIAuthenticationAware
- ubic.gemma.cli.util.CliContext
- ubic.gemma.cli.completion.CompletionGenerator
- ubic.gemma.cli.completion.CompletionSource
- org.apache.commons.cli.Converter<T,E>
- ubic.gemma.cli.util.EnumeratedByCommandConverter<T,E>
- ubic.gemma.cli.util.EnumeratedConverter<T,E>
- ubic.gemma.cli.util.EntityLocator
- ubic.gemma.cli.logging.LoggingConfigurer
Enum Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
- ubic.gemma.cli.util.CLI.CommandGroup
- ubic.gemma.cli.completion.CompletionType
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)