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.util

Class Hierarchy

• java.lang.Object
  • ubic.gemma.core.util.AbstractCLI (implements ubic.gemma.core.util.CLI)
    • ubic.gemma.core.util.AbstractSpringAwareCLI
      • ubic.gemma.core.util.AbstractCLIContextCLI
        • 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.CountObsoleteTermsCli
        • 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.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.TwoChannelMissingValueCLI
          • 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.ExternalFileGeneLoaderCLI
        • ubic.gemma.core.apps.GenericGenelistDesignGenerator
        • ubic.gemma.core.apps.GeoGrabberCli
        • ubic.gemma.core.apps.IndexGemmaCLI
        • 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.UpdatePubMedCli
      • ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
    • ubic.gemma.core.apps.MeshTermFetcherCli
  • ubic.gemma.core.apps.GemmaCLI

Interface Hierarchy

• ubic.gemma.core.util.CLI

Enum Hierarchy

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