Hierarchy For All Packages

Package Hierarchies:

• ubic.gemma.core.apps,
• ubic.gemma.core.loader.association.phenotype,
• ubic.gemma.core.loader.entrez.pubmed,
• ubic.gemma.core.logging,
• ubic.gemma.core.logging.log4j,
• ubic.gemma.core.metrics,
• ubic.gemma.core.util

Class Hierarchy

• java.lang.Object
  • ubic.gemma.core.util.AbstractCLI (implements ubic.gemma.core.util.CLI)
    • ubic.gemma.core.util.AbstractAuthenticatedCLI
      • ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
      • ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
        • ubic.gemma.core.apps.AffyProbeCollapseCli
        • ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
        • ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
        • ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
        • ubic.gemma.core.apps.ArrayDesignBlatCli
        • ubic.gemma.core.apps.ArrayDesignMapSummaryCli
        • ubic.gemma.core.apps.ArrayDesignMergeCli
        • ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
        • ubic.gemma.core.apps.ArrayDesignProbeMapperCli
        • ubic.gemma.core.apps.ArrayDesignProbeRenamerCli
        • ubic.gemma.core.apps.ArrayDesignRepeatScanCli
        • ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
        • ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
        • ubic.gemma.core.apps.BioSequenceCleanupCli
      • ubic.gemma.core.apps.BibRefUpdaterCli
      • ubic.gemma.core.apps.BlacklistCli
      • ubic.gemma.core.apps.DatabaseViewGeneratorCLI
      • ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
      • ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI
        • ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
      • ubic.gemma.core.apps.ExperimentalDesignImportCli
      • ubic.gemma.core.apps.ExperimentalDesignViewCli
      • ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
        • ubic.gemma.core.apps.AffyDataFromCelCli
        • ubic.gemma.core.apps.BatchEffectPopulationCli
        • ubic.gemma.core.apps.DeleteDiffExCli
        • ubic.gemma.core.apps.DeleteExperimentsCli
        • ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
        • ubic.gemma.core.apps.ExperimentalDesignWriterCLI
        • ubic.gemma.core.apps.ExpressionDataCorrMatCli
        • ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
        • ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
        • ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
        • ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
        • ubic.gemma.core.apps.GeeqCli
        • ubic.gemma.core.apps.LinkAnalysisCli
        • ubic.gemma.core.apps.MakeExperimentPrivateCli
        • ubic.gemma.core.apps.MakeExperimentsPublicCli
        • ubic.gemma.core.apps.OrderVectorsByDesignCli
        • ubic.gemma.core.apps.ProcessedDataComputeCLI
        • ubic.gemma.core.apps.ReplaceDataCli
        • ubic.gemma.core.apps.RNASeqBatchInfoCli
        • ubic.gemma.core.apps.RNASeqDataAddCli
        • ubic.gemma.core.apps.SplitExperimentCli
        • ubic.gemma.core.apps.SVDCli
        • ubic.gemma.core.apps.VectorMergingCli
      • ubic.gemma.core.apps.ExternalDatabaseAdderCli
      • ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI
        • ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
        • ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
        • ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli
        • ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli
        • ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli
        • ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli
      • ubic.gemma.core.apps.ExternalDatabaseOverviewCli
      • ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
      • ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
      • ubic.gemma.core.apps.FactorValueMigratorCLI
      • ubic.gemma.core.apps.GenericGenelistDesignGenerator
      • ubic.gemma.core.apps.GeoGrabberCli
      • ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
      • ubic.gemma.core.apps.LoadExpressionDataCli
      • ubic.gemma.core.apps.LoadSimpleExpressionDataCli
      • ubic.gemma.core.apps.MultifunctionalityCli
      • ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
      • ubic.gemma.core.apps.NcbiGeneLoaderCLI
      • ubic.gemma.core.apps.PubMedLoaderCli
      • ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
      • ubic.gemma.core.apps.TaxonLoaderCli
      • ubic.gemma.core.apps.UpdateEE2CCli
      • ubic.gemma.core.apps.UpdatePubMedCli
    • ubic.gemma.core.apps.FindObsoleteTermsCli
    • ubic.gemma.core.apps.IndexGemmaCLI
    • ubic.gemma.core.apps.MeshTermFetcherCli
  • ubic.gemma.core.metrics.AbstractMeterRegistryConfigurer (implements org.springframework.beans.factory.InitializingBean)
    • ubic.gemma.core.metrics.MeterRegistryCliConfigurer (implements org.springframework.context.ApplicationContextAware)
  • ubic.gemma.core.util.BashCompletionGenerator (implements ubic.gemma.core.util.CompletionGenerator)
  • ubic.gemma.core.util.ConfigurationLinter (implements org.springframework.beans.factory.InitializingBean)
  • ubic.gemma.core.util.FileUtils
  • ubic.gemma.core.util.FishCompletionGenerator (implements ubic.gemma.core.util.CompletionGenerator)
  • ubic.gemma.core.apps.GemmaCLI
  • ubic.gemma.core.logging.log4j.Log4jConfigurer (implements ubic.gemma.core.logging.LoggingConfigurer)

Interface Hierarchy

• ubic.gemma.core.util.CLI
• ubic.gemma.core.util.CompletionGenerator
• ubic.gemma.core.logging.LoggingConfigurer

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • ubic.gemma.core.apps.GemmaCLI.CommandGroup