Index (Gemma CLI 1.31.6-SNAPSHOT API)

A B C D E F G H I L M N O P R S T U V W
All Classes All Packages

A

ABORTED - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used when a AbstractCLI.doWork() is aborted.
AbstractAuthenticatedCLI - Class in ubic.gemma.core.util: Subclass this to create command line interface (CLI) tools that need authentication.
AbstractAuthenticatedCLI() - Constructor for class ubic.gemma.core.util.AbstractAuthenticatedCLI
AbstractCLI - Class in ubic.gemma.core.util: Basic implementation of the CLI interface.
AbstractCLI() - Constructor for class ubic.gemma.core.util.AbstractCLI
addAutoOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -auto option.
addAutoOption(Options, Class<? extends AuditEventType>) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -auto option for a specific AuditEventType.
addBatchOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -batchFormat and -batchOutputFile options.
addDateOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -mdate option.
addErrorObject(Object, Exception) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object based on an exception.
addErrorObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object without a cause stacktrace.
addErrorObject(Object, String, Throwable) - Method in class ubic.gemma.core.util.AbstractCLI: Add an error object with a stacktrace to indicate failure in a batch processing.
addSuccessObject(Object) - Method in class ubic.gemma.core.util.AbstractCLI
addSuccessObject(Object, String) - Method in class ubic.gemma.core.util.AbstractCLI: Add a success object to indicate success in a batch processing.
addThreadsOption(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Add the -threads option.
AffyDataFromCelCli - Class in ubic.gemma.core.apps: Add (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.
AffyDataFromCelCli() - Constructor for class ubic.gemma.core.apps.AffyDataFromCelCli
AffyProbeCollapseCli - Class in ubic.gemma.core.apps: Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
AffyProbeCollapseCli() - Constructor for class ubic.gemma.core.apps.AffyProbeCollapseCli
afterCompletion(PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
afterCompletion(PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
afterPropertiesSet() - Method in class ubic.gemma.core.util.ConfigurationLinter
allowPositionalArguments() - Method in class ubic.gemma.core.util.AbstractCLI
allowPositionalArguments() - Method in interface ubic.gemma.core.util.CLI: Indicate if this CLI allows positional arguments.
ANALYSIS - ubic.gemma.core.apps.GemmaCLI.CommandGroup
apply() - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer
apply() - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Apply pending changes to the configuration from previous LoggingConfigurer.configureAllLoggers(int) and LoggingConfigurer.configureLogger(String, int) invocations.
ArrayDesignAlternativePopulateCli - Class in ubic.gemma.core.apps: This only needs to be re-run when the mappings change.
ArrayDesignAlternativePopulateCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
ArrayDesignAnnotationFileCli - Class in ubic.gemma.core.apps: Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
ArrayDesignAnnotationFileCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
ArrayDesignAuditTrailCleanupCli - Class in ubic.gemma.core.apps: work in progress
ArrayDesignAuditTrailCleanupCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
ArrayDesignBioSequenceDetachCli - Class in ubic.gemma.core.apps: Remove all associations that this array design has with BioSequences.
ArrayDesignBioSequenceDetachCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
ArrayDesignBlatCli - Class in ubic.gemma.core.apps: Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
ArrayDesignBlatCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignBlatCli
ArrayDesignMapSummaryCli - Class in ubic.gemma.core.apps: CLI for ArrayDesignMapSummaryService
ArrayDesignMapSummaryCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
ArrayDesignMergeCli - Class in ubic.gemma.core.apps: make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
ArrayDesignMergeCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignMergeCli
ArrayDesignProbeCleanupCLI - Class in ubic.gemma.core.apps: Delete design elements (probes) that are invalid for one reason or another.
ArrayDesignProbeCleanupCLI() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
ArrayDesignProbeMapperCli - Class in ubic.gemma.core.apps: Process the blat results for an array design to map them onto genes.
ArrayDesignProbeMapperCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
ArrayDesignProbeRenamerCli - Class in ubic.gemma.core.apps: Deprecated.
renaming probes is not a good idea in general
ArrayDesignProbeRenamerCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
ArrayDesignRepeatScanCli - Class in ubic.gemma.core.apps: Runs repeatmasker on array designs.
ArrayDesignRepeatScanCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
ArrayDesignSequenceAssociationCli - Class in ubic.gemma.core.apps: Attach sequences to array design, fetching from BLAST database if requested.
ArrayDesignSequenceAssociationCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
ArrayDesignSequenceManipulatingCli - Class in ubic.gemma.core.apps: Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.
ArrayDesignSequenceManipulatingCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
ArrayDesignSubsumptionTesterCli - Class in ubic.gemma.core.apps: Test two array designs to see if one subsumes the other, and if so update their information.
ArrayDesignSubsumptionTesterCli() - Constructor for class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
auditEventService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
auditTrailService - Variable in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
auditTrailService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

B

BashCompletionGenerator - Class in ubic.gemma.core.util
BashCompletionGenerator(Set<String>) - Constructor for class ubic.gemma.core.util.BashCompletionGenerator
BatchEffectPopulationCli - Class in ubic.gemma.core.apps: For bulk processing of batch-info-fetching.
BatchEffectPopulationCli() - Constructor for class ubic.gemma.core.apps.BatchEffectPopulationCli
beforeCompletion(PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
beforeCompletion(PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
BibRefUpdaterCli - Class in ubic.gemma.core.apps: Refreshes the information in all the bibliographic references in the system.
BibRefUpdaterCli() - Constructor for class ubic.gemma.core.apps.BibRefUpdaterCli
BioSequenceCleanupCli - Class in ubic.gemma.core.apps: Goes through the biosequences for array designs in the database and removes duplicates.
BioSequenceCleanupCli() - Constructor for class ubic.gemma.core.apps.BioSequenceCleanupCli
BlacklistCli - Class in ubic.gemma.core.apps: Add entries to the blacklist
BlacklistCli() - Constructor for class ubic.gemma.core.apps.BlacklistCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.BlacklistCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeeqCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
buildOptions(Options) - Method in class ubic.gemma.core.apps.GeoGrabberCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.IndexGemmaCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.LinkAnalysisCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.MultifunctionalityCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
buildOptions(Options) - Method in class ubic.gemma.core.apps.PubMedLoaderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.ReplaceDataCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.SplitExperimentCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.SVDCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.TaxonLoaderCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.UpdateEE2CCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.UpdatePubMedCli
buildOptions(Options) - Method in class ubic.gemma.core.apps.VectorMergingCli
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
buildOptions(Options) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
buildOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI: Build option implementation.
buildStandardOptions(Options) - Method in class ubic.gemma.core.util.AbstractCLI

C

CLI - Interface in ubic.gemma.core.util: Interface for CLI tools.
CompletionGenerator - Interface in ubic.gemma.core.util
ConfigurationLinter - Class in ubic.gemma.core.util: Lint various aspects of the configuration for the CLI profile.
ConfigurationLinter() - Constructor for class ubic.gemma.core.util.ConfigurationLinter
configure(MeterRegistry) - Method in class ubic.gemma.core.metrics.MeterRegistryCliConfigurer
configureAllLoggers(int) - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer
configureAllLoggers(int) - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Set the logging level of all loggers.
configureLogger(String, int) - Method in class ubic.gemma.core.logging.log4j.Log4jConfigurer: Set up logging according to the user-selected (or default) verbosity level.
configureLogger(String, int) - Method in interface ubic.gemma.core.logging.LoggingConfigurer: Set the logging level of a specific logger.
createWriteFolder() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
CtdDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
CtdDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.

D

DatabaseViewGeneratorCLI - Class in ubic.gemma.core.apps: Simple driver of DatabaseViewGenerator.
DatabaseViewGeneratorCLI() - Constructor for class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
DeleteDiffExCli - Class in ubic.gemma.core.apps: Delete differential expression analsyes on a per-experiment basis.
DeleteDiffExCli() - Constructor for class ubic.gemma.core.apps.DeleteDiffExCli
DeleteEvidenceCLI - Class in ubic.gemma.core.loader.association.phenotype: When we need to remove all evidence from an external database, usually to reimport them after
DeleteEvidenceCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
DeleteExperimentsCli - Class in ubic.gemma.core.apps: Delete one or more experiments from the system.
DeleteExperimentsCli() - Constructor for class ubic.gemma.core.apps.DeleteExperimentsCli
DEPRECATED - ubic.gemma.core.apps.GemmaCLI.CommandGroup
DgaDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
DgaDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
DifferentialExpressionAnalysisCli - Class in ubic.gemma.core.apps: A command line interface to the DifferentialExpressionAnalysis.
DifferentialExpressionAnalysisCli() - Constructor for class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
doWork() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
doWork() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
doWork() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
doWork() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
doWork() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
doWork() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
doWork() - Method in class ubic.gemma.core.apps.BlacklistCli
doWork() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
doWork() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
doWork() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
doWork() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
doWork() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
doWork() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
doWork() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
doWork() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
doWork() - Method in class ubic.gemma.core.apps.GeeqCli
doWork() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
doWork() - Method in class ubic.gemma.core.apps.GeoGrabberCli
doWork() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
doWork() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
doWork() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
doWork() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
doWork() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
doWork() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
doWork() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
doWork() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
doWork() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
doWork() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
doWork() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
doWork() - Method in class ubic.gemma.core.apps.ReplaceDataCli
doWork() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
doWork() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
doWork() - Method in class ubic.gemma.core.apps.SplitExperimentCli
doWork() - Method in class ubic.gemma.core.apps.SVDCli
doWork() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
doWork() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
doWork() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
doWork() - Method in class ubic.gemma.core.apps.VectorMergingCli
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
doWork() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
doWork() - Method in class ubic.gemma.core.util.AbstractCLI: Command line implementation.

E

eeService - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
EvidenceImporterAbstractCLI - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
EvidenceImporterAbstractCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
EvidenceImporterCLI - Class in ubic.gemma.core.loader.association.phenotype: Class used to load evidence into Phenocarta.
EvidenceImporterCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
executeBatchTasks(Collection<? extends Runnable>) - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: Execute the given batch tasks.
executeBatchTasks(Collection<? extends Runnable>) - Method in class ubic.gemma.core.util.AbstractCLI: Execute the given batch tasks.
executeCommand(String[]) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
executeCommand(String...) - Method in class ubic.gemma.core.util.AbstractCLI: Execute the given command given CLI arguments.
executeCommand(String...) - Method in interface ubic.gemma.core.util.CLI: Execute the given command given CLI arguments.
EXPERIMENT - ubic.gemma.core.apps.GemmaCLI.CommandGroup
ExperimentalDesignImportCli - Class in ubic.gemma.core.apps
ExperimentalDesignImportCli() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignImportCli
ExperimentalDesignViewCli - Class in ubic.gemma.core.apps
ExperimentalDesignViewCli() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignViewCli
ExperimentalDesignWriterCLI - Class in ubic.gemma.core.apps: Writes out the experimental design for a given experiment.
ExperimentalDesignWriterCLI() - Constructor for class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
ExpressionDataCorrMatCli - Class in ubic.gemma.core.apps: Create correlation visualizations for expression experiments
ExpressionDataCorrMatCli() - Constructor for class ubic.gemma.core.apps.ExpressionDataCorrMatCli
ExpressionDataMatrixWriterCLI - Class in ubic.gemma.core.apps: Prints preferred data matrix to a file.
ExpressionDataMatrixWriterCLI() - Constructor for class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
ExpressionExperimentDataFileGeneratorCli - Class in ubic.gemma.core.apps
ExpressionExperimentDataFileGeneratorCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
ExpressionExperimentManipulatingCLI - Class in ubic.gemma.core.apps: Base class for CLIs that needs one or more expression experiment as an input.
ExpressionExperimentManipulatingCLI() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
ExpressionExperimentPlatformSwitchCli - Class in ubic.gemma.core.apps: Switch the array design used to the merged one.
ExpressionExperimentPlatformSwitchCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
ExpressionExperimentPrimaryPubCli - Class in ubic.gemma.core.apps: Update the primary publication for experiments.
ExpressionExperimentPrimaryPubCli() - Constructor for class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
expressionExperiments - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
ExternalDatabaseAdderCli - Class in ubic.gemma.core.apps: Add a new external database, but requires editing the code to do so.
ExternalDatabaseAdderCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseAdderCli
ExternalDatabaseEvidenceImporterAbstractCLI - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
ExternalDatabaseEvidenceImporterAbstractCLI() - Constructor for class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
ExternalDatabaseOverviewCli - Class in ubic.gemma.core.apps
ExternalDatabaseOverviewCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
ExternalDatabaseUpdaterCli - Class in ubic.gemma.core.apps
ExternalDatabaseUpdaterCli() - Constructor for class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
ExternalFileGeneLoaderCLI - Class in ubic.gemma.core.apps: CLI for loading genes from a non NCBI files.
ExternalFileGeneLoaderCLI() - Constructor for class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI

F

FactorValueMigratorCLI - Class in ubic.gemma.core.apps: Deprecated.
this will be removed as soon as all the old-style characteristics are migrated
FactorValueMigratorCLI() - Constructor for class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
FAILURE - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a failed AbstractCLI.doWork() execution.
FAILURE_FROM_ERROR_OBJECTS - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a successful doWork execution that resulted in failed error objects.
FileUtils - Class in ubic.gemma.core.util
FileUtils() - Constructor for class ubic.gemma.core.util.FileUtils
findGeneByOfficialSymbol(String, Taxon) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
FindObsoleteTermsCli - Class in ubic.gemma.core.apps
FindObsoleteTermsCli() - Constructor for class ubic.gemma.core.apps.FindObsoleteTermsCli
findTypeOfEvidence() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.

Look at all Headers and identify them to determine the type of evidence
FishCompletionGenerator - Class in ubic.gemma.core.util: Generates fish completion script.
FishCompletionGenerator(Set<String>) - Constructor for class ubic.gemma.core.util.FishCompletionGenerator
FOOTER - Static variable in class ubic.gemma.core.util.AbstractCLI
force - Variable in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

G

GeeqCli - Class in ubic.gemma.core.apps: Generate or update GEEQ scores
GeeqCli() - Constructor for class ubic.gemma.core.apps.GeeqCli
GemmaCLI - Class in ubic.gemma.core.apps: Generic command line for Gemma.
GemmaCLI() - Constructor for class ubic.gemma.core.apps.GemmaCLI
GemmaCLI.CommandGroup - Enum in ubic.gemma.core.apps
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
generateCompletion(Options, PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.core.util.FishCompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.core.util.BashCompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in interface ubic.gemma.core.util.CompletionGenerator
generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.core.util.FishCompletionGenerator
GenericGenelistDesignGenerator - Class in ubic.gemma.core.apps: Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.
GenericGenelistDesignGenerator() - Constructor for class ubic.gemma.core.apps.GenericGenelistDesignGenerator
geneService - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
GeoGrabberCli - Class in ubic.gemma.core.apps: Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.
GeoGrabberCli() - Constructor for class ubic.gemma.core.apps.GeoGrabberCli
getArrayDesignReportService() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getArrayDesignService() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getArrayDesignsToProcess() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getAutoSeekEventType() - Method in class ubic.gemma.core.util.AbstractCLI
getBean(Class<T>) - Method in class ubic.gemma.core.util.AbstractCLI: Deprecated.
getBean(String, Class<T>) - Method in class ubic.gemma.core.util.AbstractCLI: Deprecated.
Use Autowired to specify your dependencies, this is just a wrapper around the current BeanFactory.
getCommandGroup() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getCommandGroup() - Method in class ubic.gemma.core.apps.BlacklistCli
getCommandGroup() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getCommandGroup() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getCommandGroup() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getCommandGroup() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getCommandGroup() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getCommandGroup() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getCommandGroup() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getCommandGroup() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getCommandGroup() - Method in class ubic.gemma.core.apps.SVDCli
getCommandGroup() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getCommandGroup() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getCommandGroup() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getCommandGroup() - Method in class ubic.gemma.core.apps.VectorMergingCli
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getCommandGroup() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getCommandGroup() - Method in interface ubic.gemma.core.util.CLI: Obtain the command group for this CLI.
getCommandName() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getCommandName() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
getCommandName() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
getCommandName() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getCommandName() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getCommandName() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
getCommandName() - Method in class ubic.gemma.core.apps.BlacklistCli
getCommandName() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getCommandName() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
getCommandName() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
getCommandName() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getCommandName() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
getCommandName() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getCommandName() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getCommandName() - Method in class ubic.gemma.core.apps.GeeqCli
getCommandName() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getCommandName() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getCommandName() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getCommandName() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
getCommandName() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getCommandName() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getCommandName() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
getCommandName() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
getCommandName() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getCommandName() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getCommandName() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getCommandName() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getCommandName() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getCommandName() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getCommandName() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getCommandName() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getCommandName() - Method in class ubic.gemma.core.apps.SVDCli
getCommandName() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getCommandName() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getCommandName() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getCommandName() - Method in class ubic.gemma.core.apps.VectorMergingCli
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getCommandName() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getCommandName() - Method in interface ubic.gemma.core.util.CLI: A short memorable name for the command that can be used to locate this class.
getLimitingDate() - Method in class ubic.gemma.core.util.AbstractCLI
getLoader() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getNumThreads() - Method in class ubic.gemma.core.util.AbstractCLI
getOptions() - Method in class ubic.gemma.core.util.AbstractCLI
getOptions() - Method in interface ubic.gemma.core.util.CLI: Obtain the options for the CLI.
getShortDesc() - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
getShortDesc() - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignAuditTrailCleanupCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignMapSummaryCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
getShortDesc() - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
getShortDesc() - Method in class ubic.gemma.core.apps.BatchEffectPopulationCli
getShortDesc() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
getShortDesc() - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
getShortDesc() - Method in class ubic.gemma.core.apps.BlacklistCli
getShortDesc() - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
getShortDesc() - Method in class ubic.gemma.core.apps.DeleteDiffExCli
getShortDesc() - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
getShortDesc() - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionDataCorrMatCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
getShortDesc() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
getShortDesc() - Method in class ubic.gemma.core.apps.GeeqCli
getShortDesc() - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
getShortDesc() - Method in class ubic.gemma.core.apps.GeoGrabberCli
getShortDesc() - Method in class ubic.gemma.core.apps.IndexGemmaCLI
getShortDesc() - Method in class ubic.gemma.core.apps.LinkAnalysisCli
getShortDesc() - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.MakeExperimentPrivateCli
getShortDesc() - Method in class ubic.gemma.core.apps.MakeExperimentsPublicCli
getShortDesc() - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
getShortDesc() - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
getShortDesc() - Method in class ubic.gemma.core.apps.OrderVectorsByDesignCli
getShortDesc() - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
getShortDesc() - Method in class ubic.gemma.core.apps.PubMedLoaderCli
getShortDesc() - Method in class ubic.gemma.core.apps.ReplaceDataCli
getShortDesc() - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
getShortDesc() - Method in class ubic.gemma.core.apps.SplitExperimentCli
getShortDesc() - Method in class ubic.gemma.core.apps.SVDCli
getShortDesc() - Method in class ubic.gemma.core.apps.TaxonLoaderCli
getShortDesc() - Method in class ubic.gemma.core.apps.UpdateEE2CCli
getShortDesc() - Method in class ubic.gemma.core.apps.UpdatePubMedCli
getShortDesc() - Method in class ubic.gemma.core.apps.VectorMergingCli
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterCLI
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
getShortDesc() - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
getShortDesc() - Method in interface ubic.gemma.core.util.CLI: Obtain a short description for this command explaining what it does.
getTaxonByName(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
getTaxonByName(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
GwasDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
GwasDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.

H

HEADER - Static variable in class ubic.gemma.core.util.AbstractCLI

I

IndexGemmaCLI - Class in ubic.gemma.core.apps
IndexGemmaCLI() - Constructor for class ubic.gemma.core.apps.IndexGemmaCLI
init() - Method in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.

load all needed services and initialize data structures
isAutoSeek() - Method in class ubic.gemma.core.util.AbstractCLI
isSubsumedOrMerged(ArrayDesign) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

L

LinkAnalysisCli - Class in ubic.gemma.core.apps: Commandline tool to conduct link (coexpression) analysis.
LinkAnalysisCli() - Constructor for class ubic.gemma.core.apps.LinkAnalysisCli
LoadEvidenceForClassifier - Class in ubic.gemma.core.loader.association.phenotype: Retrieve information used for classifying Phenocarta evidence quality.
LoadEvidenceForClassifier() - Constructor for class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
LoadExpressionDataCli - Class in ubic.gemma.core.apps: Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.
LoadExpressionDataCli() - Constructor for class ubic.gemma.core.apps.LoadExpressionDataCli
LoadSimpleExpressionDataCli - Class in ubic.gemma.core.apps: Command Line tools for loading the expression experiment in flat files
LoadSimpleExpressionDataCli() - Constructor for class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
locateArrayDesign(String) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
locateExpressionExperiment(String) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
log - Static variable in class ubic.gemma.core.util.AbstractCLI
Log4jConfigurer - Class in ubic.gemma.core.logging.log4j: Implementation of LoggingConfigurer for Log4j.
Log4jConfigurer() - Constructor for class ubic.gemma.core.logging.log4j.Log4jConfigurer
LoggingConfigurer - Interface in ubic.gemma.core.logging: Simple interface for configuring logging levels.

M

main(String[]) - Static method in class ubic.gemma.core.apps.GemmaCLI
MakeExperimentPrivateCli - Class in ubic.gemma.core.apps
MakeExperimentPrivateCli() - Constructor for class ubic.gemma.core.apps.MakeExperimentPrivateCli
MakeExperimentsPublicCli - Class in ubic.gemma.core.apps: Make data sets public.
MakeExperimentsPublicCli() - Constructor for class ubic.gemma.core.apps.MakeExperimentsPublicCli
MeshTermFetcherCli - Class in ubic.gemma.core.apps: Deprecated.
should not be part of Gemma main code
MeshTermFetcherCli() - Constructor for class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
METADATA - ubic.gemma.core.apps.GemmaCLI.CommandGroup
MeterRegistryCliConfigurer - Class in ubic.gemma.core.metrics: This configurer adds two tags: environment='cli' and user to the given meter registry.
MeterRegistryCliConfigurer(MeterRegistry) - Constructor for class ubic.gemma.core.metrics.MeterRegistryCliConfigurer
MISC - ubic.gemma.core.apps.GemmaCLI.CommandGroup
MultifunctionalityCli - Class in ubic.gemma.core.apps
MultifunctionalityCli() - Constructor for class ubic.gemma.core.apps.MultifunctionalityCli

N

NCBIGene2GOAssociationLoaderCLI - Class in ubic.gemma.core.apps: Load GO -> gene associations from NCBI.
NCBIGene2GOAssociationLoaderCLI() - Constructor for class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
NcbiGeneLoaderCLI - Class in ubic.gemma.core.apps: Command line interface to gene parsing and loading
NcbiGeneLoaderCLI() - Constructor for class ubic.gemma.core.apps.NcbiGeneLoaderCLI
noNeedToRun(Auditable, Class<? extends AuditEventType>) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI

O

OmimDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
OmimDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
OrderVectorsByDesignCli - Class in ubic.gemma.core.apps: Use to change the order of the values to match the experimental design.
OrderVectorsByDesignCli() - Constructor for class ubic.gemma.core.apps.OrderVectorsByDesignCli

P

PHENOTYPES - ubic.gemma.core.apps.GemmaCLI.CommandGroup
PLATFORM - ubic.gemma.core.apps.GemmaCLI.CommandGroup
ppUtil - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.
ProcessedDataComputeCLI - Class in ubic.gemma.core.apps: Prepare the "processed" expression data vectors, and can also do batch correction.
ProcessedDataComputeCLI() - Constructor for class ubic.gemma.core.apps.ProcessedDataComputeCLI
processGeneList() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI: Main entry point to service class which reads a gene file and persists the genes in that file.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.AffyDataFromCelCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.AffyProbeCollapseCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignAnnotationFileCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignBioSequenceDetachCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignBlatCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignMergeCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeCleanupCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli: See 'configure' for how the other options are handled.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignProbeRenamerCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignRepeatScanCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceAssociationCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ArrayDesignSubsumptionTesterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BioSequenceCleanupCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.BlacklistCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DatabaseViewGeneratorCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DeleteExperimentsCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.DifferentialExpressionAnalysisCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignImportCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignViewCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExperimentalDesignWriterCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionDataMatrixWriterCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentDataFileGeneratorCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentManipulatingCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentPlatformSwitchCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExpressionExperimentPrimaryPubCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseAdderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseOverviewCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI: This method is called at the end of processCommandLine
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.FactorValueMigratorCLI: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.FindObsoleteTermsCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GeeqCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GenericGenelistDesignGenerator
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.GeoGrabberCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.IndexGemmaCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LinkAnalysisCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LoadExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.LoadSimpleExpressionDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.MeshTermFetcherCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.MultifunctionalityCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.NCBIGene2GOAssociationLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ProcessedDataComputeCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.PubMedLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.ReplaceDataCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.RNASeqDataAddCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.SplitExperimentCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.TaxonLoaderCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.UpdateEE2CCli
processOptions(CommandLine) - Method in class ubic.gemma.core.apps.UpdatePubMedCli
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.DeleteEvidenceCLI
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.LoadEvidenceForClassifier
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
processOptions(CommandLine) - Method in class ubic.gemma.core.loader.entrez.pubmed.PubMedSearcher
processOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractCLI: Process command line options.
processStandardOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: You must override this method to process any options you added.
processStandardOptions(CommandLine) - Method in class ubic.gemma.core.util.AbstractCLI: Somewhat annoying: This causes subclasses to be unable to safely use 'h', 'p', 'u' and 'P' etc.
promptConfirmationOrAbort(String) - Method in class ubic.gemma.core.util.AbstractCLI: Prompt the user for a confirmation or raise an exception to abort the AbstractCLI.doWork() method.
PubMedLoaderCli - Class in ubic.gemma.core.apps: Load PubMed files from XML files -- not used routinely!
PubMedLoaderCli() - Constructor for class ubic.gemma.core.apps.PubMedLoaderCli
PubMedSearcher - Class in ubic.gemma.core.loader.entrez.pubmed: Simple application to perform pubmed searches from a list of terms, and persist the results in the database.

R

readListFileToStrings(String) - Static method in class ubic.gemma.core.util.FileUtils: may be tab-delimited, only first column used, commented (#) lines are ignored.
ReplaceDataCli - Class in ubic.gemma.core.apps: Replace data in an existing data set.
ReplaceDataCli() - Constructor for class ubic.gemma.core.apps.ReplaceDataCli
requireLogin() - Method in class ubic.gemma.core.apps.ArrayDesignAlternativePopulateCli
requireLogin() - Method in class ubic.gemma.core.apps.ArrayDesignProbeMapperCli
requireLogin() - Method in class ubic.gemma.core.apps.BibRefUpdaterCli
requireLogin() - Method in class ubic.gemma.core.apps.BlacklistCli
requireLogin() - Method in class ubic.gemma.core.apps.ExternalDatabaseUpdaterCli
requireLogin() - Method in class ubic.gemma.core.apps.ExternalFileGeneLoaderCLI
requireLogin() - Method in class ubic.gemma.core.apps.MultifunctionalityCli
requireLogin() - Method in class ubic.gemma.core.apps.NcbiGeneLoaderCLI
requireLogin() - Method in class ubic.gemma.core.util.AbstractAuthenticatedCLI: Indicate if the command requires authentication.
RgdDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
RgdDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli: Deprecated.
RNASeqBatchInfoCli - Class in ubic.gemma.core.apps: Deprecated.
this should not be necessary and the regular batch population tool can be used instead.
RNASeqBatchInfoCli() - Constructor for class ubic.gemma.core.apps.RNASeqBatchInfoCli: Deprecated.
RNASeqDataAddCli - Class in ubic.gemma.core.apps: Designed to add count and/or RPKM data to a data set that has only meta-data.
RNASeqDataAddCli() - Constructor for class ubic.gemma.core.apps.RNASeqDataAddCli

S

setAllowPositionalArguments(boolean) - Method in class ubic.gemma.core.util.AbstractCLI: Allow positional arguments to be specified.
setApplicationContext(ApplicationContext) - Method in class ubic.gemma.core.metrics.MeterRegistryCliConfigurer
SfariDatabaseImporterCli - Class in ubic.gemma.core.loader.association.phenotype: Deprecated.
SfariDatabaseImporterCli() - Constructor for class ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli: Deprecated.
shouldRun(Date, ArrayDesign, Class<? extends ArrayDesignAnalysisEvent>) - Method in class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
SplitExperimentCli - Class in ubic.gemma.core.apps: Split an experiment into parts based on an experimental factor
SplitExperimentCli() - Constructor for class ubic.gemma.core.apps.SplitExperimentCli
SUCCESS - Static variable in class ubic.gemma.core.util.AbstractCLI: Exit code used for a successful AbstractCLI.doWork() execution.
SVDCli - Class in ubic.gemma.core.apps
SVDCli() - Constructor for class ubic.gemma.core.apps.SVDCli
SYSTEM - ubic.gemma.core.apps.GemmaCLI.CommandGroup

T

TaxonLoaderCli - Class in ubic.gemma.core.apps
TaxonLoaderCli() - Constructor for class ubic.gemma.core.apps.TaxonLoaderCli
taxonService - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.

U

ubic.gemma.core.apps - package ubic.gemma.core.apps
ubic.gemma.core.loader.association.phenotype - package ubic.gemma.core.loader.association.phenotype
ubic.gemma.core.loader.entrez.pubmed - package ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.logging - package ubic.gemma.core.logging
ubic.gemma.core.logging.log4j - package ubic.gemma.core.logging.log4j
ubic.gemma.core.metrics - package ubic.gemma.core.metrics
ubic.gemma.core.util - package ubic.gemma.core.util
UpdateEE2CCli - Class in ubic.gemma.core.apps
UpdateEE2CCli() - Constructor for class ubic.gemma.core.apps.UpdateEE2CCli
UpdatePubMedCli - Class in ubic.gemma.core.apps: Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.
UpdatePubMedCli() - Constructor for class ubic.gemma.core.apps.UpdatePubMedCli

V

valueOf(String) - Static method in enum ubic.gemma.core.apps.GemmaCLI.CommandGroup: Returns the enum constant of this type with the specified name.
values() - Static method in enum ubic.gemma.core.apps.GemmaCLI.CommandGroup: Returns an array containing the constants of this enum type, in the order they are declared.
VectorMergingCli - Class in ubic.gemma.core.apps: For experiments that used multiple array designs, merge the expression profiles
VectorMergingCli() - Constructor for class ubic.gemma.core.apps.VectorMergingCli

W

writeFolder - Variable in class ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI: Deprecated.

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