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

A

abort(String) - Method in class ubic.gemma.cli.util.AbstractCLI

Abort the execution of the CLI with the given message.

ABORTED - Static variable in class ubic.gemma.cli.util.AbstractCLI

Exit code used when a AbstractCLI.doWork() is aborted.

AbstractAuthenticatedCLI - Class in ubic.gemma.cli.util

Subclass this to create command line interface (CLI) tools that need authentication.

AbstractAuthenticatedCLI() - Constructor for class ubic.gemma.cli.util.AbstractAuthenticatedCLI

AbstractAutoSeekingCLI<T extends ubic.gemma.model.common.auditAndSecurity.Auditable> - Class in ubic.gemma.cli.util

Provide auto-seeking capabilities to a CLI.

AbstractAutoSeekingCLI(Class<T>) - Constructor for class ubic.gemma.cli.util.AbstractAutoSeekingCLI

AbstractCLI - Class in ubic.gemma.cli.util

Basic implementation of the CLI interface.

AbstractCLI() - Constructor for class ubic.gemma.cli.util.AbstractCLI

AbstractCompletionGenerator - Class in ubic.gemma.cli.completion

AbstractCompletionGenerator() - Constructor for class ubic.gemma.cli.completion.AbstractCompletionGenerator

AbstractDelegatingExecutorService - Class in ubic.gemma.cli.batch

A delegating executor service inspired by DelegatingSecurityContextExecutorService.

AbstractDelegatingExecutorService(ExecutorService) - Constructor for class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

addAutoOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Add the -auto option.

addAutoOption(Options, Class<? extends AuditEventType>) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Add the -auto option for a specific AuditEventType.

addAutoOption(Options, String, String, String, String, String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils

Add an option with three possible values: true, false, or null.

addBatchOption(Options) - Method in class ubic.gemma.cli.util.AbstractCLI

Add the -batchFormat and -batchOutputFile options.

addCommaDelimitedPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying a comma-delimited list of platforms.

addDatasetOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying a dataset.

addDateOption(String, String, String, Options) - Static method in class ubic.gemma.cli.util.OptionsUtils

Add a date option with support for fuzzy dates (i.e. one month ago).

addEnumOption(Options, String, String, String, Class<T>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Add an enumerated option with localized descriptions.

addEnumOption(Options, String, String, String, Class<T>, EnumMap<T, MessageSourceResolvable>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Add an enumerated option with descriptions.

addErrorObject(Serializable, Exception) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Add an error object based on an exception.

addErrorObject(Serializable, Exception) - Method in class ubic.gemma.cli.util.AbstractCLI

Add an error object based on an exception.

addErrorObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Add an error object without a cause stacktrace.

addErrorObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI

Add an error object without a cause stacktrace.

addErrorObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Add an error object with a stacktrace to indicate failure in a batch processing.

addErrorObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractCLI

Add an error object with a stacktrace to indicate failure in a batch processing.

addErrorObject(T, Exception) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addErrorObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addErrorObject(T, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addExperimentSetOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying an EE set.

addForceOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addForceOption(Options, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addGenericPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying a generic platform.

addLimitingDateOption(Options) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Add the -mdate option.

addPlatformOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying a platform.

addSingleExperimentOption(Options, String, String, boolean, String) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Add an option that is only available in single-experiment mode.

addSingleExperimentOption(Options, Option) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Add an option that is only available in single-experiment mode.

addSuccessObject(Serializable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

addSuccessObject(Serializable) - Method in class ubic.gemma.cli.util.AbstractCLI

addSuccessObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Add a success object to indicate success in a batch processing.

addSuccessObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI

Add a success object to indicate success in a batch processing.

addSuccessObject(T) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addSuccessObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addTaxonOption(Options, String, String, String) - Static method in class ubic.gemma.cli.util.EntityOptionsUtils

Add an option for supplying a taxon.

addThreadsOption(Options) - Method in class ubic.gemma.cli.util.AbstractCLI

Add the -threads option.

addWarningObject(Serializable, String) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

addWarningObject(Serializable, String) - Method in class ubic.gemma.cli.util.AbstractCLI

addWarningObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

addWarningObject(Serializable, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractCLI

Add a warning object with a stacktrace to indicate a recoverable failure in a batch processing.

addWarningObject(T, String) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addWarningObject(T, String, Throwable) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

AffyDataFromCelCli - Class in ubic.gemma.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.apps.AffyDataFromCelCli

AffyProbeCollapseCli - Class in ubic.gemma.apps

Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.

AffyProbeCollapseCli() - Constructor for class ubic.gemma.apps.AffyProbeCollapseCli

afterCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator

afterCompletion(PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator

Executed after all completions have been generated.

afterCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator

afterPropertiesSet() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

afterPropertiesSet() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

afterPropertiesSet() - Method in class ubic.gemma.apps.GeoGrabberCli

afterPropertiesSet() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

allOf(Predicate<CommandLine>...) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that all the given predicates are true.

allowPositionalArguments() - Method in class ubic.gemma.cli.util.AbstractCLI

allowPositionalArguments() - Method in interface ubic.gemma.cli.util.CLI

Indicate if this CLI allows positional arguments.

ANALYSIS - ubic.gemma.cli.util.CLI.CommandGroup

anyOf(Predicate<CommandLine>...) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that at least one of the given predicate is true.

apply() - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer

apply() - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Apply pending changes to the configuration.

apply(String) - Method in class ubic.gemma.cli.util.EnumConverter

apply(String) - Method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter

apply(String) - Method in class ubic.gemma.cli.util.EnumeratedStringConverter

ArrayDesignAlternativePopulateCli - Class in ubic.gemma.apps

This only needs to be re-run when the mappings change.

ArrayDesignAlternativePopulateCli() - Constructor for class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

ArrayDesignAnnotationFileCli - Class in ubic.gemma.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.apps.ArrayDesignAnnotationFileCli

ArrayDesignAuditTrailCleanupCli - Class in ubic.gemma.apps

work in progress

ArrayDesignAuditTrailCleanupCli() - Constructor for class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli

ArrayDesignBioSequenceDetachCli - Class in ubic.gemma.apps

Remove all associations that this array design has with BioSequences.

ArrayDesignBioSequenceDetachCli() - Constructor for class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

ArrayDesignBlatCli - Class in ubic.gemma.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.apps.ArrayDesignBlatCli

ArrayDesignMapSummaryCli - Class in ubic.gemma.apps

CLI for ArrayDesignMapSummaryService

ArrayDesignMapSummaryCli() - Constructor for class ubic.gemma.apps.ArrayDesignMapSummaryCli

ArrayDesignMergeCli - Class in ubic.gemma.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.apps.ArrayDesignMergeCli

ArrayDesignProbeCleanupCLI - Class in ubic.gemma.apps

Delete design elements (probes) that are invalid for one reason or another.

ArrayDesignProbeCleanupCLI() - Constructor for class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

ArrayDesignProbeMapperCli - Class in ubic.gemma.apps

Process the blat results for an array design to map them onto genes.

ArrayDesignProbeMapperCli() - Constructor for class ubic.gemma.apps.ArrayDesignProbeMapperCli

ArrayDesignProbeRenamerCli - Class in ubic.gemma.apps

Deprecated.

renaming probes is not a good idea in general

ArrayDesignProbeRenamerCli() - Constructor for class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

ArrayDesignRepeatScanCli - Class in ubic.gemma.apps

Runs repeatmasker on array designs.

ArrayDesignRepeatScanCli() - Constructor for class ubic.gemma.apps.ArrayDesignRepeatScanCli

ArrayDesignSequenceAssociationCli - Class in ubic.gemma.apps

Attach sequences to array design, fetching from BLAST database if requested.

ArrayDesignSequenceAssociationCli() - Constructor for class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

ArrayDesignSequenceManipulatingCli - Class in ubic.gemma.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.apps.ArrayDesignSequenceManipulatingCli

ArrayDesignSubsumptionTesterCli - Class in ubic.gemma.apps

Test two array designs to see if one subsumes the other, and if so update their information.

ArrayDesignSubsumptionTesterCli() - Constructor for class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

auditEventService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

auditEventService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

auditTrailService - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

auditTrailService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

authenticate(String, String) - Method in class ubic.gemma.cli.authentication.CLIAuthenticationManager

authenticateAnonymously() - Method in class ubic.gemma.cli.authentication.CLIAuthenticationManager

awaitBatchExecutorService() - Method in class ubic.gemma.cli.util.AbstractCLI

Await the completion of all batch tasks.

awaitTermination(long, TimeUnit) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

B

BashCompletionGenerator - Class in ubic.gemma.cli.completion

BashCompletionGenerator(String, Set<String>) - Constructor for class ubic.gemma.cli.completion.BashCompletionGenerator

BatchEffectPopulationCli - Class in ubic.gemma.apps

For bulk processing of batch-info-fetching.

BatchEffectPopulationCli() - Constructor for class ubic.gemma.apps.BatchEffectPopulationCli

BatchTaskExecutorService - Class in ubic.gemma.cli.batch

A task executor that automatically reports errors in batch tasks.

BatchTaskExecutorService(ExecutorService, BatchTaskProgressReporter) - Constructor for class ubic.gemma.cli.batch.BatchTaskExecutorService

BatchTaskProcessingResult - Class in ubic.gemma.cli.batch

Represents an individual result in a batch processing.

BatchTaskProgressReporter - Class in ubic.gemma.cli.batch

Report progress on batch tasks.

BatchTaskProgressReporter(BatchTaskSummaryWriter) - Constructor for class ubic.gemma.cli.batch.BatchTaskProgressReporter

BatchTaskSummaryWriter - Interface in ubic.gemma.cli.batch

beforeCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator

beforeCompletion(PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator

Executed before any completions has been generated.

beforeCompletion(PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator

BibRefUpdaterCli - Class in ubic.gemma.apps

Refreshes the information in all the bibliographic references in the system.

BibRefUpdaterCli() - Constructor for class ubic.gemma.apps.BibRefUpdaterCli

BioSequenceCleanupCli - Class in ubic.gemma.apps

Goes through the biosequences for array designs in the database and removes duplicates.

BioSequenceCleanupCli() - Constructor for class ubic.gemma.apps.BioSequenceCleanupCli

BlacklistCli - Class in ubic.gemma.apps

Add entries to the blacklist

BlacklistCli() - Constructor for class ubic.gemma.apps.BlacklistCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.AffyDataFromCelCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.BatchEffectPopulationCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DeleteExperimentsCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DetectQuantitationTypeCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.GeeqCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.LinkAnalysisCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.LockExpressionDataFileCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.RefreshExperimentCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.ReplaceDataCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.RNASeqDataAddCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SplitExperimentCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.SVDCli

buildExperimentOptions(Options) - Method in class ubic.gemma.apps.VectorMergingCli

buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli

buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli

buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli

buildExperimentVectorsOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataWriterCli

buildOptions(Options) - Method in class ubic.gemma.apps.AffyProbeCollapseCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignBlatCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignMergeCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

buildOptions(Options) - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

buildOptions(Options) - Method in class ubic.gemma.apps.BibRefUpdaterCli

buildOptions(Options) - Method in class ubic.gemma.apps.BioSequenceCleanupCli

buildOptions(Options) - Method in class ubic.gemma.apps.BlacklistCli

buildOptions(Options) - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

buildOptions(Options) - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

buildOptions(Options) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli

buildOptions(Options) - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

buildOptions(Options) - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

buildOptions(Options) - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

buildOptions(Options) - Method in class ubic.gemma.apps.FindObsoleteTermsCli

buildOptions(Options) - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

buildOptions(Options) - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

buildOptions(Options) - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

buildOptions(Options) - Method in class ubic.gemma.apps.GeoGrabberCli

buildOptions(Options) - Method in class ubic.gemma.apps.IndexGemmaCLI

buildOptions(Options) - Method in class ubic.gemma.apps.InitializeDatabaseCli

buildOptions(Options) - Method in class ubic.gemma.apps.LoadExpressionDataCli

buildOptions(Options) - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

buildOptions(Options) - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

buildOptions(Options) - Method in class ubic.gemma.apps.MultifunctionalityCli

buildOptions(Options) - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

buildOptions(Options) - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

buildOptions(Options) - Method in class ubic.gemma.apps.ProtocolAdderCli

buildOptions(Options) - Method in class ubic.gemma.apps.ProtocolDeleterCli

buildOptions(Options) - Method in class ubic.gemma.apps.PubMedLoaderCli

buildOptions(Options) - Method in class ubic.gemma.apps.PubMedSearcher

buildOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataDownloaderCli

buildOptions(Options) - Method in class ubic.gemma.apps.SingleCellDataTransformCli

buildOptions(Options) - Method in class ubic.gemma.apps.TaxonLoaderCli

buildOptions(Options) - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli

buildOptions(Options) - Method in class ubic.gemma.apps.UpdateDatabaseCli

buildOptions(Options) - Method in class ubic.gemma.apps.UpdateEe2AdCli

buildOptions(Options) - Method in class ubic.gemma.apps.UpdateEE2CCli

buildOptions(Options) - Method in class ubic.gemma.apps.UpdateGene2CsCli

buildOptions(Options) - Method in class ubic.gemma.apps.UpdatePubMedCli

buildOptions(Options) - Method in class ubic.gemma.cli.util.AbstractCLI

Build option implementation.

C

clearAuthentication() - Method in interface ubic.gemma.cli.authentication.CLIAuthenticationAware

clearAuthentication() - Method in class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator

CLI - Interface in ubic.gemma.cli.util

Interface for CLI tools.

CLI.CommandGroup - Enum in ubic.gemma.cli.util

CLIAuthenticationAware - Interface in ubic.gemma.cli.authentication

Interface for a component that should receive the username/password authentication token from the CLI.

CLIAuthenticationManager - Class in ubic.gemma.cli.authentication

Manages authentication from the CLI.

CLIAuthenticationManager(ManualAuthenticationService, List<CLIAuthenticationAware>) - Constructor for class ubic.gemma.cli.authentication.CLIAuthenticationManager

CliContext - Interface in ubic.gemma.cli.util

close() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Print out a summary of what the program did.

close() - Method in interface ubic.gemma.cli.batch.BatchTaskSummaryWriter

Close the writer and write any remaining results.

close() - Method in class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter

close() - Method in class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter

close() - Method in class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter

close() - Method in class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter

close() - Method in class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter

CompleteCli - Class in ubic.gemma.apps

This CLI provide various runtime completions that can be re-used by other CLIs.

CompleteCli() - Constructor for class ubic.gemma.apps.CompleteCli

Completion() - Constructor for class ubic.gemma.cli.completion.CompletionSource.Completion

CompletionGenerator - Interface in ubic.gemma.cli.completion

CompletionSource - Interface in ubic.gemma.cli.completion

Defines a source of completions.

CompletionSource.Completion - Class in ubic.gemma.cli.completion

CompletionType - Enum in ubic.gemma.cli.completion

CompletionUtils - Class in ubic.gemma.cli.completion

Utilities for generating completions.

CompletionUtils() - Constructor for class ubic.gemma.cli.completion.CompletionUtils

CompositeBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch

CompositeBatchTaskSummaryWriter(List<BatchTaskSummaryWriter>) - Constructor for class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter

ConfigurationLinter - Class in ubic.gemma.cli.config

Lint various aspects of the configuration for the CLI profile.

ConfigurationLinter() - Constructor for class ubic.gemma.cli.config.ConfigurationLinter

configure(MeterRegistry) - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer

configureAllLoggers(int) - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer

configureAllLoggers(int) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Set the logging level of all loggers.

configureAllLoggers(String) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Set the logging level of all loggers using a named level.

configureLogger(String, int) - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer

Set up logging according to the user-selected (or default) verbosity level.

configureLogger(String, int) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Set the logging level of a specific logger.

configureLogger(String, String) - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Set the logging level of a specific logger using a named level.

createBatchTaskExecutorService() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

createBatchTaskExecutorService() - Method in class ubic.gemma.cli.util.AbstractCLI

Create an ExecutorService to be used for running batch tasks.

D

DatabaseViewGeneratorCLI - Class in ubic.gemma.apps

Simple driver of DatabaseViewGenerator.

DatabaseViewGeneratorCLI() - Constructor for class ubic.gemma.apps.DatabaseViewGeneratorCLI

DATASET - ubic.gemma.cli.completion.CompletionType

DeleteDiffExCli - Class in ubic.gemma.apps

Delete differential expression analsyes on a per-experiment basis.

DeleteDiffExCli() - Constructor for class ubic.gemma.apps.DeleteDiffExCli

DeleteExperimentsCli - Class in ubic.gemma.apps

Delete one or more experiments from the system.

DeleteExperimentsCli() - Constructor for class ubic.gemma.apps.DeleteExperimentsCli

DEPRECATED - ubic.gemma.cli.util.CLI.CommandGroup

DetectQuantitationTypeCli - Class in ubic.gemma.apps

DetectQuantitationTypeCli() - Constructor for class ubic.gemma.apps.DetectQuantitationTypeCli

DifferentialExpressionAnalysisCli - Class in ubic.gemma.apps

A command line interface to the DifferentialExpressionAnalysis.

DifferentialExpressionAnalysisCli() - Constructor for class ubic.gemma.apps.DifferentialExpressionAnalysisCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.AffyProbeCollapseCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignBlatCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignMergeCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.BibRefUpdaterCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.BioSequenceCleanupCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.BlacklistCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.CompleteCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

doAuthenticatedWork() - Method in class ubic.gemma.apps.DeleteExperimentsCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

Main entry point to service class which reads a gene file and persists the genes in that file.

doAuthenticatedWork() - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

doAuthenticatedWork() - Method in class ubic.gemma.apps.FindObsoleteTermsCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

doAuthenticatedWork() - Method in class ubic.gemma.apps.GeoGrabberCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.LinkAnalysisCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.LoadExpressionDataCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.MultifunctionalityCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

doAuthenticatedWork() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolAdderCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolDeleterCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.ProtocolListCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.PubMedLoaderCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.PubMedSearcher

doAuthenticatedWork() - Method in class ubic.gemma.apps.TaxonLoaderCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateEe2AdCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateEE2CCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdateGene2CsCli

doAuthenticatedWork() - Method in class ubic.gemma.apps.UpdatePubMedCli

doAuthenticatedWork() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

doWork() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

doWork() - Method in class ubic.gemma.apps.IndexGemmaCLI

doWork() - Method in class ubic.gemma.apps.InitializeDatabaseCli

doWork() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli

doWork() - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

doWork() - Method in class ubic.gemma.apps.SingleCellDataDownloaderCli

doWork() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

doWork() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli

doWork() - Method in class ubic.gemma.apps.UpdateDatabaseCli

doWork() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

doWork() - Method in class ubic.gemma.cli.util.AbstractCLI

Command line implementation.

E

eeService - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

EESET - ubic.gemma.cli.completion.CompletionType

entityLocator - Variable in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

entityLocator - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

EntityLocator - Interface in ubic.gemma.cli.util

Locate various entities using identifiers supplied by the CLI.

EntityLocatorImpl - Class in ubic.gemma.cli.util

EntityLocatorImpl() - Constructor for class ubic.gemma.cli.util.EntityLocatorImpl

EntityOptionsUtils - Class in ubic.gemma.cli.util

Utilities for adding options to the CLI that can subsequently be retrieved with EntityLocator.

EntityOptionsUtils() - Constructor for class ubic.gemma.cli.util.EntityOptionsUtils

entityUrlBuilder - Variable in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

EnumConverter<T extends Enum<T>> - Class in ubic.gemma.cli.util

Convert Enum to string.

EnumeratedByCommandConverter<T,E extends Throwable> - Interface in ubic.gemma.cli.util

This interface is implemented by Converter that can use an external command to get possible values.

EnumeratedByCommandStringConverter - Class in ubic.gemma.cli.util

EnumeratedConverter<T,E extends Throwable> - Interface in ubic.gemma.cli.util

This interface is implemented by converters that can enumerate their possible values.

EnumeratedStringConverter - Class in ubic.gemma.cli.util

A string converter that can only convert from a finite set of possible values.

execute(Runnable) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

executeCommand(CliContext) - Method in class ubic.gemma.cli.util.AbstractCLI

Execute the given command given CLI arguments.

executeCommand(CliContext) - Method in interface ubic.gemma.cli.util.CLI

Execute the given command given CLI arguments.

EXPERIMENT - ubic.gemma.cli.util.CLI.CommandGroup

ExperimentalDesignImportCli - Class in ubic.gemma.apps

ExperimentalDesignImportCli() - Constructor for class ubic.gemma.apps.ExperimentalDesignImportCli

ExperimentalDesignViewCli - Class in ubic.gemma.apps

ExperimentalDesignViewCli() - Constructor for class ubic.gemma.apps.ExperimentalDesignViewCli

ExperimentalDesignWriterCLI - Class in ubic.gemma.apps

Writes out the experimental design for a given experiment.

ExperimentalDesignWriterCLI() - Constructor for class ubic.gemma.apps.ExperimentalDesignWriterCLI

ExpressionDataCorrMatCli - Class in ubic.gemma.apps

Create correlation visualizations for expression experiments

ExpressionDataCorrMatCli() - Constructor for class ubic.gemma.apps.ExpressionDataCorrMatCli

ExpressionDataMatrixWriterCLI - Class in ubic.gemma.apps

Prints preferred data matrix to a file.

ExpressionDataMatrixWriterCLI() - Constructor for class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

ExpressionExperimentDataFileGeneratorCli - Class in ubic.gemma.apps

ExpressionExperimentDataFileGeneratorCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

ExpressionExperimentDataUpdaterCli - Class in ubic.gemma.apps

Update GEO data for an experiment.

ExpressionExperimentDataUpdaterCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli

ExpressionExperimentManipulatingCLI - Class in ubic.gemma.apps

Base class for CLIs that needs one or more expression experiment as an input.

ExpressionExperimentManipulatingCLI() - Constructor for class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

ExpressionExperimentMetadataChangelogEntryAdderCli - Class in ubic.gemma.apps

CLI tool for adding manual entries to the changelog file of an experiment.

ExpressionExperimentMetadataChangelogEntryAdderCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

ExpressionExperimentMetadataChangelogViewerCli - Class in ubic.gemma.apps

CLI tool for viewing the changelog file of an experiment.

ExpressionExperimentMetadataChangelogViewerCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli

ExpressionExperimentMetadataFileAdderCli - Class in ubic.gemma.apps

Add a metadata file to an experiment and record an entry in the changelog file.

ExpressionExperimentMetadataFileAdderCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

ExpressionExperimentPlatformSwitchCli - Class in ubic.gemma.apps

Switch the array design used to the merged one.

ExpressionExperimentPlatformSwitchCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

ExpressionExperimentPrimaryPubCli - Class in ubic.gemma.apps

Update the primary publication for experiments.

ExpressionExperimentPrimaryPubCli() - Constructor for class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

ExpressionExperimentVectorsManipulatingCli<T extends ubic.gemma.model.expression.bioAssayData.DataVector> - Class in ubic.gemma.apps

Base class for CLI tools that manipulate expression experiment vectors.

ExpressionExperimentVectorsManipulatingCli(Class<T>) - Constructor for class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

EXTERNAL_DATABASE - ubic.gemma.cli.completion.CompletionType

ExternalDatabaseAdderCli - Class in ubic.gemma.apps

Add a new external database, but requires editing the code to do so.

ExternalDatabaseAdderCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseAdderCli

ExternalDatabaseOverviewCli - Class in ubic.gemma.apps

ExternalDatabaseOverviewCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseOverviewCli

ExternalDatabaseUpdaterCli - Class in ubic.gemma.apps

ExternalDatabaseUpdaterCli() - Constructor for class ubic.gemma.apps.ExternalDatabaseUpdaterCli

ExternalFileGeneLoaderCLI - Class in ubic.gemma.apps

CLI for loading genes from a non NCBI files.

ExternalFileGeneLoaderCLI() - Constructor for class ubic.gemma.apps.ExternalFileGeneLoaderCLI

F

FactorValueMigratorCLI - Class in ubic.gemma.apps

Deprecated.

this will be removed as soon as all the old-style characteristics are migrated

FactorValueMigratorCLI() - Constructor for class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

FAILURE - Static variable in class ubic.gemma.cli.util.AbstractCLI

Exit code used for a failed AbstractCLI.doWork() execution.

FAILURE_FROM_ERROR_OBJECTS - Static variable in class ubic.gemma.cli.util.AbstractCLI

Exit code used for a successful doWork execution that resulted in failed error objects.

FileUtils - Class in ubic.gemma.cli.util

FileUtils() - Constructor for class ubic.gemma.cli.util.FileUtils

FindObsoleteTermsCli - Class in ubic.gemma.apps

FindObsoleteTermsCli() - Constructor for class ubic.gemma.apps.FindObsoleteTermsCli

FishCompletionGenerator - Class in ubic.gemma.cli.completion

Generates fish completion script.

FishCompletionGenerator(String, Set<String>, MessageSource, Locale) - Constructor for class ubic.gemma.cli.completion.FishCompletionGenerator

FixOntologyTermLabelsCli - Class in ubic.gemma.apps

FixOntologyTermLabelsCli() - Constructor for class ubic.gemma.apps.FixOntologyTermLabelsCli

FOOTER - Static variable in class ubic.gemma.cli.util.HelpUtils

FORCE_OPTION - Static variable in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

formatExperiment(BioAssaySet) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Render an experiment to string, with special handling in case of an uninitialized proxy.

G

GeeqCli - Class in ubic.gemma.apps

Generate or update GEEQ scores

GeeqCli() - Constructor for class ubic.gemma.apps.GeeqCli

GEMMA_CLI_EXE - Static variable in class ubic.gemma.cli.main.GemmaCLI

Name of the Gemma CLI executable.

GemmaCLI - Class in ubic.gemma.cli.main

Generic command line for Gemma.

GemmaCLI() - Constructor for class ubic.gemma.cli.main.GemmaCLI

gemmaRestApiClient(String) - Method in class ubic.gemma.cli.config.GemmaRestApiClientConfig

GemmaRestApiClientAuthenticator - Class in ubic.gemma.cli.authentication

GemmaRestApiClientAuthenticator(GemmaRestApiClient) - Constructor for class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator

GemmaRestApiClientConfig - Class in ubic.gemma.cli.config

GemmaRestApiClientConfig() - Constructor for class ubic.gemma.cli.config.GemmaRestApiClientConfig

generateCompleteCommand(CompletionType, String...) - Static method in class ubic.gemma.cli.completion.CompletionUtils

Generate a complete command suitable for EnumeratedByCommandConverter.

generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator

generateCompletion(Options, PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator

Generate completion for the given options.

generateCompletion(Options, PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator

GenerateDatabaseUpdateCli - Class in ubic.gemma.apps

Generate a database update script.

GenerateDatabaseUpdateCli() - Constructor for class ubic.gemma.apps.GenerateDatabaseUpdateCli

generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.cli.completion.BashCompletionGenerator

generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in interface ubic.gemma.cli.completion.CompletionGenerator

Generate completions for the given subcommand.

generateSubcommandCompletion(String, Options, String, boolean, PrintWriter) - Method in class ubic.gemma.cli.completion.FishCompletionGenerator

GenericGenelistDesignGenerator - Class in ubic.gemma.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.apps.GenericGenelistDesignGenerator

GeoGrabberCli - Class in ubic.gemma.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.apps.GeoGrabberCli

getAllLoggerNames() - Method in class ubic.gemma.cli.logging.log4j.Log4jConfigurer

getAllLoggerNames() - Method in interface ubic.gemma.cli.logging.LoggingConfigurer

Obtain the list of all logger names.

getApplicationContext() - Method in class ubic.gemma.cli.util.AbstractCLI

Obtain the application context.

getArguments() - Method in interface ubic.gemma.cli.util.CliContext

Obtain the command line arguments for the command.

getArguments() - Method in class ubic.gemma.cli.util.SystemCliContext

getArrayDesignReportService() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

getArrayDesignService() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

getArrayDesignsToProcess() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

getAutoOptionValue(CommandLine, String, String) - Static method in class ubic.gemma.cli.util.OptionsUtils

getAutoSeekEventType() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Indicate the event to be used for auto-seeking.

getBatchTaskExecutor() - Method in class ubic.gemma.cli.util.AbstractCLI

Obtain an executor for running batch tasks.

getCliContext() - Method in class ubic.gemma.cli.util.AbstractCLI

Obtain the CLI context.

getCommandAliases() - Method in class ubic.gemma.cli.util.AbstractCLI

getCommandAliases() - Method in interface ubic.gemma.cli.util.CLI

A list of aliases for the command that can be used to locate this class.

getCommandGroup() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

getCommandGroup() - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli

getCommandGroup() - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

getCommandGroup() - Method in class ubic.gemma.apps.BibRefUpdaterCli

getCommandGroup() - Method in class ubic.gemma.apps.BlacklistCli

getCommandGroup() - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

getCommandGroup() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

getCommandGroup() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

getCommandGroup() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

getCommandGroup() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

getCommandGroup() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

getCommandGroup() - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

getCommandGroup() - Method in class ubic.gemma.apps.FindObsoleteTermsCli

getCommandGroup() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

getCommandGroup() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

getCommandGroup() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

getCommandGroup() - Method in class ubic.gemma.apps.GeoGrabberCli

getCommandGroup() - Method in class ubic.gemma.apps.IndexGemmaCLI

getCommandGroup() - Method in class ubic.gemma.apps.InitializeDatabaseCli

getCommandGroup() - Method in class ubic.gemma.apps.LoadExpressionDataCli

getCommandGroup() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

getCommandGroup() - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

getCommandGroup() - Method in class ubic.gemma.apps.MultifunctionalityCli

getCommandGroup() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

getCommandGroup() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

getCommandGroup() - Method in class ubic.gemma.apps.PubMedLoaderCli

getCommandGroup() - Method in class ubic.gemma.apps.PubMedSearcher

getCommandGroup() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

getCommandGroup() - Method in class ubic.gemma.apps.TaxonLoaderCli

getCommandGroup() - Method in class ubic.gemma.apps.UpdateDatabaseCli

getCommandGroup() - Method in class ubic.gemma.apps.UpdateEe2AdCli

getCommandGroup() - Method in class ubic.gemma.apps.UpdateEE2CCli

getCommandGroup() - Method in class ubic.gemma.apps.UpdateGene2CsCli

getCommandGroup() - Method in class ubic.gemma.apps.UpdatePubMedCli

getCommandGroup() - Method in class ubic.gemma.cli.util.AbstractCLI

getCommandGroup() - Method in interface ubic.gemma.cli.util.CLI

Obtain the command group for this CLI.

getCommandName() - Method in class ubic.gemma.apps.AffyDataFromCelCli

getCommandName() - Method in class ubic.gemma.apps.AffyProbeCollapseCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignBlatCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignMergeCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

getCommandName() - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

getCommandName() - Method in class ubic.gemma.apps.BatchEffectPopulationCli

getCommandName() - Method in class ubic.gemma.apps.BibRefUpdaterCli

getCommandName() - Method in class ubic.gemma.apps.BioSequenceCleanupCli

getCommandName() - Method in class ubic.gemma.apps.BlacklistCli

getCommandName() - Method in class ubic.gemma.apps.CompleteCli

getCommandName() - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

getCommandName() - Method in class ubic.gemma.apps.DeleteDiffExCli

getCommandName() - Method in class ubic.gemma.apps.DeleteExperimentsCli

getCommandName() - Method in class ubic.gemma.apps.DetectQuantitationTypeCli

getCommandName() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

getCommandName() - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI

getCommandName() - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

getCommandName() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli

getCommandName() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

getCommandName() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

getCommandName() - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

getCommandName() - Method in class ubic.gemma.apps.FindObsoleteTermsCli

getCommandName() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

getCommandName() - Method in class ubic.gemma.apps.GeeqCli

getCommandName() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

getCommandName() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

getCommandName() - Method in class ubic.gemma.apps.GeoGrabberCli

getCommandName() - Method in class ubic.gemma.apps.IndexGemmaCLI

getCommandName() - Method in class ubic.gemma.apps.InitializeDatabaseCli

getCommandName() - Method in class ubic.gemma.apps.LinkAnalysisCli

getCommandName() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli

getCommandName() - Method in class ubic.gemma.apps.ListQuantitationTypesCli

getCommandName() - Method in class ubic.gemma.apps.LoadExpressionDataCli

getCommandName() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

getCommandName() - Method in class ubic.gemma.apps.LockExpressionDataFileCli

getCommandName() - Method in class ubic.gemma.apps.MakeExperimentPrivateCli

getCommandName() - Method in class ubic.gemma.apps.MakeExperimentsPublicCli

getCommandName() - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

getCommandName() - Method in class ubic.gemma.apps.MultifunctionalityCli

getCommandName() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

getCommandName() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

getCommandName() - Method in class ubic.gemma.apps.OrderVectorsByDesignCli

getCommandName() - Method in class ubic.gemma.apps.ProcessedDataComputeCLI

getCommandName() - Method in class ubic.gemma.apps.ProcessedDataDeleterCli

getCommandName() - Method in class ubic.gemma.apps.ProtocolAdderCli

getCommandName() - Method in class ubic.gemma.apps.ProtocolDeleterCli

getCommandName() - Method in class ubic.gemma.apps.ProtocolListCli

getCommandName() - Method in class ubic.gemma.apps.PubMedLoaderCli

getCommandName() - Method in class ubic.gemma.apps.PubMedSearcher

getCommandName() - Method in class ubic.gemma.apps.RawDataDeleterCli

getCommandName() - Method in class ubic.gemma.apps.RawExpressionDataWriterCli

getCommandName() - Method in class ubic.gemma.apps.RefreshExperimentCli

getCommandName() - Method in class ubic.gemma.apps.ReplaceDataCli

getCommandName() - Method in class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

getCommandName() - Method in class ubic.gemma.apps.RNASeqDataAddCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataAggregateDeleterCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataDeleterCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataDownloaderCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellDataWriterCli

getCommandName() - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli

getCommandName() - Method in class ubic.gemma.apps.SplitExperimentCli

getCommandName() - Method in class ubic.gemma.apps.SVDCli

getCommandName() - Method in class ubic.gemma.apps.TaxonLoaderCli

getCommandName() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli

getCommandName() - Method in class ubic.gemma.apps.UpdateDatabaseCli

getCommandName() - Method in class ubic.gemma.apps.UpdateEe2AdCli

getCommandName() - Method in class ubic.gemma.apps.UpdateEE2CCli

getCommandName() - Method in class ubic.gemma.apps.UpdateGene2CsCli

getCommandName() - Method in class ubic.gemma.apps.UpdatePubMedCli

getCommandName() - Method in class ubic.gemma.apps.VectorMergingCli

getCommandName() - Method in class ubic.gemma.cli.util.AbstractCLI

getCommandName() - Method in interface ubic.gemma.cli.util.CLI

A short memorable name for the command that can be used to locate this class.

getCommandNameOrAliasUsed() - Method in interface ubic.gemma.cli.util.CliContext

Command name or alias used to invoke the command, or null if this was invoked using the fully qualified class name.

getCommandNameOrAliasUsed() - Method in class ubic.gemma.cli.util.SystemCliContext

getCompletedTasks() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Obtain the number of completed tasks (either with a success or failure result).

getCompletions() - Method in interface ubic.gemma.cli.completion.CompletionSource

getCompletions() - Method in class ubic.gemma.cli.completion.LoggerCompletionSource

getCompletions() - Method in class ubic.gemma.cli.completion.SettingsCompletionSource

getConsole() - Method in interface ubic.gemma.cli.util.CliContext

Obtain the console, if available.

getConsole() - Method in class ubic.gemma.cli.util.SystemCliContext

getEnumOptionValue(CommandLine, String) - Static method in class ubic.gemma.cli.util.OptionsUtils

Obtain the value of an enumerated option.

getEnumOptionValue(CommandLine, String, Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Obtain the value of an enumerated option and if present, make sure that it satisfies a predicate.

getEnvironment() - Method in interface ubic.gemma.cli.util.CliContext

Obtain the environment variables for the command.

getEnvironment() - Method in class ubic.gemma.cli.util.SystemCliContext

getErrorStream() - Method in interface ubic.gemma.cli.util.CliContext

getErrorStream() - Method in class ubic.gemma.cli.util.SystemCliContext

getHelpFooter() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

getHelpFooter() - Method in class ubic.gemma.cli.util.AbstractCLI

Include a detailed help footer in the --help menu.

getInputStream() - Method in interface ubic.gemma.cli.util.CliContext

getInputStream() - Method in class ubic.gemma.cli.util.SystemCliContext

getLimitingDate() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Obtain the limiting date (i.e. starting date at which entities should be processed).

getLoader() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

getNumThreads() - Method in class ubic.gemma.cli.util.AbstractCLI

getOptions() - Method in class ubic.gemma.cli.util.AbstractCLI

getOptions() - Method in interface ubic.gemma.cli.util.CLI

Obtain the options for the CLI.

getOptionValue(CommandLine, String, Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Obtain the value of an option and if present, make sure that it satisfies a predicate.

getOptionValues(CommandLine, String, Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

getOutputStream() - Method in interface ubic.gemma.cli.util.CliContext

getOutputStream() - Method in class ubic.gemma.cli.util.SystemCliContext

getParsedOptionValue(CommandLine, String, Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

getPossibleValues() - Method in class ubic.gemma.cli.util.EnumConverter

getPossibleValues() - Method in interface ubic.gemma.cli.util.EnumeratedConverter

Obtain a list of possible values that the converter can convert to EnumeratedConverter.

getPossibleValues() - Method in class ubic.gemma.cli.util.EnumeratedStringConverter

getPossibleValuesCommand() - Method in interface ubic.gemma.cli.util.EnumeratedByCommandConverter

Command that can be used to get possible values.

getPossibleValuesCommand() - Method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter

getRemainingTasks() - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService

Obtain the number of completed batch tasks.

getShortDesc() - Method in class ubic.gemma.apps.AffyDataFromCelCli

getShortDesc() - Method in class ubic.gemma.apps.AffyProbeCollapseCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignAuditTrailCleanupCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignBlatCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignMapSummaryCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignMergeCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

getShortDesc() - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

getShortDesc() - Method in class ubic.gemma.apps.BatchEffectPopulationCli

getShortDesc() - Method in class ubic.gemma.apps.BibRefUpdaterCli

getShortDesc() - Method in class ubic.gemma.apps.BioSequenceCleanupCli

getShortDesc() - Method in class ubic.gemma.apps.BlacklistCli

getShortDesc() - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

getShortDesc() - Method in class ubic.gemma.apps.DeleteDiffExCli

getShortDesc() - Method in class ubic.gemma.apps.DeleteExperimentsCli

getShortDesc() - Method in class ubic.gemma.apps.DetectQuantitationTypeCli

getShortDesc() - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

getShortDesc() - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI

getShortDesc() - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

getShortDesc() - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli

getShortDesc() - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

getShortDesc() - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

getShortDesc() - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

getShortDesc() - Method in class ubic.gemma.apps.FindObsoleteTermsCli

getShortDesc() - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

getShortDesc() - Method in class ubic.gemma.apps.GeeqCli

getShortDesc() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

getShortDesc() - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

getShortDesc() - Method in class ubic.gemma.apps.GeoGrabberCli

getShortDesc() - Method in class ubic.gemma.apps.IndexGemmaCLI

getShortDesc() - Method in class ubic.gemma.apps.InitializeDatabaseCli

getShortDesc() - Method in class ubic.gemma.apps.LinkAnalysisCli

getShortDesc() - Method in class ubic.gemma.apps.ListExpressionDataFIleLocksCli

getShortDesc() - Method in class ubic.gemma.apps.ListQuantitationTypesCli

getShortDesc() - Method in class ubic.gemma.apps.LoadExpressionDataCli

getShortDesc() - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

getShortDesc() - Method in class ubic.gemma.apps.LockExpressionDataFileCli

getShortDesc() - Method in class ubic.gemma.apps.MakeExperimentPrivateCli

getShortDesc() - Method in class ubic.gemma.apps.MakeExperimentsPublicCli

getShortDesc() - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

getShortDesc() - Method in class ubic.gemma.apps.MultifunctionalityCli

getShortDesc() - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

getShortDesc() - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

getShortDesc() - Method in class ubic.gemma.apps.OrderVectorsByDesignCli

getShortDesc() - Method in class ubic.gemma.apps.ProcessedDataComputeCLI

getShortDesc() - Method in class ubic.gemma.apps.ProcessedDataDeleterCli

getShortDesc() - Method in class ubic.gemma.apps.ProtocolAdderCli

getShortDesc() - Method in class ubic.gemma.apps.ProtocolDeleterCli

getShortDesc() - Method in class ubic.gemma.apps.ProtocolListCli

getShortDesc() - Method in class ubic.gemma.apps.PubMedLoaderCli

getShortDesc() - Method in class ubic.gemma.apps.PubMedSearcher

getShortDesc() - Method in class ubic.gemma.apps.RawDataDeleterCli

getShortDesc() - Method in class ubic.gemma.apps.RawExpressionDataWriterCli

getShortDesc() - Method in class ubic.gemma.apps.RefreshExperimentCli

getShortDesc() - Method in class ubic.gemma.apps.ReplaceDataCli

getShortDesc() - Method in class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

getShortDesc() - Method in class ubic.gemma.apps.RNASeqDataAddCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataAggregateDeleterCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataDeleterCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataDownloaderCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellDataWriterCli

getShortDesc() - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli

getShortDesc() - Method in class ubic.gemma.apps.SplitExperimentCli

getShortDesc() - Method in class ubic.gemma.apps.SVDCli

getShortDesc() - Method in class ubic.gemma.apps.TaxonLoaderCli

getShortDesc() - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli

getShortDesc() - Method in class ubic.gemma.apps.UpdateDatabaseCli

getShortDesc() - Method in class ubic.gemma.apps.UpdateEe2AdCli

getShortDesc() - Method in class ubic.gemma.apps.UpdateEE2CCli

getShortDesc() - Method in class ubic.gemma.apps.UpdateGene2CsCli

getShortDesc() - Method in class ubic.gemma.apps.UpdatePubMedCli

getShortDesc() - Method in class ubic.gemma.apps.VectorMergingCli

getShortDesc() - Method in class ubic.gemma.cli.util.AbstractCLI

getShortDesc() - Method in interface ubic.gemma.cli.util.CLI

Obtain a short description for this command explaining what it does.

getUsage() - Method in class ubic.gemma.apps.CompleteCli

getUsage() - Method in class ubic.gemma.apps.SingleCellDataTransformCli

Adjust usage to reflect the transformation-specific options.

getUsage() - Method in class ubic.gemma.cli.util.AbstractCLI

Describe the intended usage for the command.

getWriter() - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

H

hasErrorObjects() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Indicate if error objects have been reported.

hasOption(CommandLine, String, Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Check if an option is present, and if so make sure that the predicate is satisfied.

HEADER - Static variable in class ubic.gemma.cli.util.HelpUtils

HelpUtils - Class in ubic.gemma.cli.util

HelpUtils() - Constructor for class ubic.gemma.cli.util.HelpUtils

I

IndexGemmaCLI - Class in ubic.gemma.apps

IndexGemmaCLI() - Constructor for class ubic.gemma.apps.IndexGemmaCLI

InitializeDatabaseCli - Class in ubic.gemma.apps

Initialize the database.

InitializeDatabaseCli() - Constructor for class ubic.gemma.apps.InitializeDatabaseCli

invokeAll(Collection<? extends Callable<T>>) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

invokeAll(Collection<? extends Callable<T>>, long, TimeUnit) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

invokeAny(Collection<? extends Callable<T>>) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

invokeAny(Collection<? extends Callable<T>>, long, TimeUnit) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

isAbortOnError() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Indicate if this CLI should abort on error or move on to the next experiment.

isAutoSeek() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Indicate if auto-seek is enabled.

isFileOption(Option) - Method in class ubic.gemma.cli.completion.AbstractCompletionGenerator

isForce() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Check if forcing is enabled.

isShutdown() - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

isSubsumedOrMerged(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

isTerminated() - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

L

LinkAnalysisCli - Class in ubic.gemma.apps

Commandline tool to conduct link (coexpression) analysis.

LinkAnalysisCli() - Constructor for class ubic.gemma.apps.LinkAnalysisCli

ListExpressionDataFIleLocksCli - Class in ubic.gemma.apps

List all locks within Gemma's data directories.

ListExpressionDataFIleLocksCli() - Constructor for class ubic.gemma.apps.ListExpressionDataFIleLocksCli

ListQuantitationTypesCli - Class in ubic.gemma.apps

ListQuantitationTypesCli() - Constructor for class ubic.gemma.apps.ListQuantitationTypesCli

LoadExpressionDataCli - Class in ubic.gemma.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.apps.LoadExpressionDataCli

LoadSimpleExpressionDataCli - Class in ubic.gemma.apps

Command Line tools for loading the expression experiment in flat files

LoadSimpleExpressionDataCli() - Constructor for class ubic.gemma.apps.LoadSimpleExpressionDataCli

locateArrayDesign(String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateArrayDesign(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateBioAssay(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateBioAssay(ExpressionExperiment, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateBioAssay(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateBioAssay(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateCellLevelCharacteristics(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateCellTypeAssignment(ExpressionExperiment, QuantitationType, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateExperimentalFactor(ExpressionExperiment, String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateExperimentalFactor(ExpressionExperiment, String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateExpressionExperiment(String, boolean) - Method in interface ubic.gemma.cli.util.EntityLocator

locateExpressionExperiment(String, boolean) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

Attempt to locate an experiment using the given identifier.

locateProtocol(String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateProtocol(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateQuantitationType(ExpressionExperiment, String, Class<? extends T>) - Method in interface ubic.gemma.cli.util.EntityLocator

locateQuantitationType(ExpressionExperiment, String, Class<? extends T>) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateQuantitationType(ExpressionExperiment, String, Collection<Class<? extends T>>) - Method in interface ubic.gemma.cli.util.EntityLocator

locateQuantitationType(ExpressionExperiment, String, Collection<Class<? extends T>>) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

locateTaxon(String) - Method in interface ubic.gemma.cli.util.EntityLocator

locateTaxon(String) - Method in class ubic.gemma.cli.util.EntityLocatorImpl

LockExpressionDataFileCli - Class in ubic.gemma.apps

This CLI allows one to lock an experiment data or metadata file.

LockExpressionDataFileCli() - Constructor for class ubic.gemma.apps.LockExpressionDataFileCli

log - Variable in class ubic.gemma.cli.util.AbstractCLI

Log4jConfigurer - Class in ubic.gemma.cli.logging.log4j

Implementation of LoggingConfigurer for Log4j.

Log4jConfigurer() - Constructor for class ubic.gemma.cli.logging.log4j.Log4jConfigurer

LoggerCompletionSource - Class in ubic.gemma.cli.completion

LoggerCompletionSource(LoggingConfigurer) - Constructor for class ubic.gemma.cli.completion.LoggerCompletionSource

LoggingBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch

Task summary writer that logs the result of a batch task to a logger.

LoggingBatchTaskSummaryWriter(String) - Constructor for class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter

LoggingBatchTaskSummaryWriter(String, boolean) - Constructor for class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter

LoggingConfigurer - Interface in ubic.gemma.cli.logging

Simple interface for configuring logging levels.

M

main(String[]) - Static method in class ubic.gemma.cli.main.GemmaCLI

MakeExperimentPrivateCli - Class in ubic.gemma.apps

MakeExperimentPrivateCli() - Constructor for class ubic.gemma.apps.MakeExperimentPrivateCli

MakeExperimentsPublicCli - Class in ubic.gemma.apps

Make data sets public.

MakeExperimentsPublicCli() - Constructor for class ubic.gemma.apps.MakeExperimentsPublicCli

MeshTermFetcherCli - Class in ubic.gemma.apps

Deprecated.

should not be part of Gemma main code

MeshTermFetcherCli() - Constructor for class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

METADATA - ubic.gemma.cli.util.CLI.CommandGroup

MeterRegistryCliConfigurer - Class in ubic.gemma.cli.metrics

This configurer adds two tags: environment='cli' and user to the given meter registry.

MeterRegistryCliConfigurer(MeterRegistry) - Constructor for class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer

MINIMAL - Static variable in class ubic.gemma.apps.GeoGrabberCli

Preset when seeking records.

MISC - ubic.gemma.cli.util.CLI.CommandGroup

MultifunctionalityCli - Class in ubic.gemma.apps

MultifunctionalityCli() - Constructor for class ubic.gemma.apps.MultifunctionalityCli

N

NAMED_LEVELS - Static variable in interface ubic.gemma.cli.logging.LoggingConfigurer

NCBIGene2GOAssociationLoaderCLI - Class in ubic.gemma.apps

Load GO -> gene associations from NCBI.

NCBIGene2GOAssociationLoaderCLI() - Constructor for class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

NcbiGeneLoaderCLI - Class in ubic.gemma.apps

Command line interface to gene parsing and loading

NcbiGeneLoaderCLI() - Constructor for class ubic.gemma.apps.NcbiGeneLoaderCLI

needToRun(Date, ArrayDesign, Class<? extends ArrayDesignAnalysisEvent>) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.

needToRun(Date, ArrayDesign, Class<? extends ArrayDesignAnalysisEvent>) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

noNeedToRun(T, Class<? extends AuditEventType>) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Check if the given auditable can be skipped.

noNeedToRun(ExpressionExperiment, Class<? extends AuditEventType>) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

noneOf(Predicate<CommandLine>...) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that none of the given predicates are true.

NUMBERED_LEVELS - Static variable in interface ubic.gemma.cli.logging.LoggingConfigurer

O

of(Class<T>) - Static method in class ubic.gemma.cli.util.EnumConverter

of(Class<T>, EnumMap<T, MessageSourceResolvable>) - Static method in class ubic.gemma.cli.util.EnumConverter

of(String...) - Static method in class ubic.gemma.cli.util.EnumeratedByCommandStringConverter

of(String...) - Static method in class ubic.gemma.cli.util.EnumeratedStringConverter

of(Map<String, MessageSourceResolvable>) - Static method in class ubic.gemma.cli.util.EnumeratedStringConverter

onApplicationEvent(ContextRefreshedEvent) - Method in class ubic.gemma.cli.config.ConfigurationLinter

OptionsUtils - Class in ubic.gemma.cli.util

OptionsUtils() - Constructor for class ubic.gemma.cli.util.OptionsUtils

OrderVectorsByDesignCli - Class in ubic.gemma.apps

Use to change the order of the values to match the experimental design.

OrderVectorsByDesignCli() - Constructor for class ubic.gemma.apps.OrderVectorsByDesignCli

P

PLATFORM - ubic.gemma.cli.completion.CompletionType

PLATFORM - ubic.gemma.cli.util.CLI.CommandGroup

preprocessBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Pre-process BioAssays.

preprocessBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.LinkAnalysisCli

preprocessBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

printHelp(PrintWriter, String, Options, String, String) - Static method in class ubic.gemma.cli.util.HelpUtils

processBioAssaySet(BioAssaySet) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Process a BioAssaySet.

processBioAssaySet(BioAssaySet) - Method in class ubic.gemma.apps.MakeExperimentPrivateCli

processBioAssaySet(BioAssaySet) - Method in class ubic.gemma.apps.MakeExperimentsPublicCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.AffyDataFromCelCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Process multiple BioAssaySet.

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.RNASeqDataAddCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

processBioAssaySets(Collection<BioAssaySet>) - Method in class ubic.gemma.apps.SingleCellDataWriterCli

ProcessedDataComputeCLI - Class in ubic.gemma.apps

Prepare the "processed" expression data vectors, and can also do batch correction.

ProcessedDataComputeCLI() - Constructor for class ubic.gemma.apps.ProcessedDataComputeCLI

ProcessedDataDeleterCli - Class in ubic.gemma.apps

ProcessedDataDeleterCli() - Constructor for class ubic.gemma.apps.ProcessedDataDeleterCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.AffyDataFromCelCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DeleteExperimentsCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DetectQuantitationTypeCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.GeeqCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.LinkAnalysisCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.LockExpressionDataFileCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.RefreshExperimentCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.ReplaceDataCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.RNASeqDataAddCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

processExperimentOptions(CommandLine) - Method in class ubic.gemma.apps.SplitExperimentCli

processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli

processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli

processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli

processExperimentVectorsOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataWriterCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.AffyDataFromCelCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.BatchEffectPopulationCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DeleteDiffExCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DeleteExperimentsCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DetectQuantitationTypeCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.DifferentialExpressionAnalysisCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExperimentalDesignImportCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExperimentalDesignWriterCLI

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionDataCorrMatCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionDataMatrixWriterCLI

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentDataFileGeneratorCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentDataUpdaterCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Process an ExpressionExperiment.

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogEntryAdderCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataChangelogViewerCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentMetadataFileAdderCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentPlatformSwitchCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentPrimaryPubCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.GeeqCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.LinkAnalysisCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ListQuantitationTypesCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.LockExpressionDataFileCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.OrderVectorsByDesignCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ProcessedDataComputeCLI

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RefreshExperimentCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.ReplaceDataCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.RNASeqDataAddCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellDataLoaderCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SplitExperimentCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.SVDCli

processExpressionExperiment(ExpressionExperiment) - Method in class ubic.gemma.apps.VectorMergingCli

processExpressionExperimentSubSet(ExpressionExperimentSubSet) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Process an ExpressionExperimentSubSet.

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

Process a set of vectors identified by a QuantitationType.

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ListQuantitationTypesCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.ProcessedDataDeleterCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.RawDataDeleterCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.RawExpressionDataWriterCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataAggregateDeleterCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataAggregatorCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataDeleterCli

processExpressionExperimentVectors(ExpressionExperiment, QuantitationType) - Method in class ubic.gemma.apps.SingleCellDataWriterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.AffyProbeCollapseCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignAlternativePopulateCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignAnnotationFileCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignBioSequenceDetachCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignBlatCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignMergeCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignProbeCleanupCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignProbeMapperCli

See 'configure' for how the other options are handled.

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignProbeRenamerCli

Deprecated.

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignRepeatScanCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSequenceAssociationCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ArrayDesignSubsumptionTesterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.BibRefUpdaterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.BioSequenceCleanupCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.BlacklistCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.CompleteCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.DatabaseViewGeneratorCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExperimentalDesignViewCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseAdderCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseOverviewCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalDatabaseUpdaterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ExternalFileGeneLoaderCLI

This method is called at the end of processCommandLine

processOptions(CommandLine) - Method in class ubic.gemma.apps.FactorValueMigratorCLI

Deprecated.

processOptions(CommandLine) - Method in class ubic.gemma.apps.FindObsoleteTermsCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.FixOntologyTermLabelsCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.GenerateDatabaseUpdateCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.GenericGenelistDesignGenerator

processOptions(CommandLine) - Method in class ubic.gemma.apps.GeoGrabberCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.IndexGemmaCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.InitializeDatabaseCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.LoadExpressionDataCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.LoadSimpleExpressionDataCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.MeshTermFetcherCli

Deprecated.

processOptions(CommandLine) - Method in class ubic.gemma.apps.MultifunctionalityCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.NCBIGene2GOAssociationLoaderCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.NcbiGeneLoaderCLI

processOptions(CommandLine) - Method in class ubic.gemma.apps.ProtocolAdderCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.ProtocolDeleterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.PubMedLoaderCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.PubMedSearcher

processOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataDownloaderCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.SingleCellDataTransformCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.TaxonLoaderCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UnifiedOntologyUpdaterCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateDatabaseCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateEe2AdCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateEE2CCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdateGene2CsCli

processOptions(CommandLine) - Method in class ubic.gemma.apps.UpdatePubMedCli

processOptions(CommandLine) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

processOptions(CommandLine) - Method in class ubic.gemma.cli.util.AbstractCLI

Process command line options.

processOtherBioAssaySet(BioAssaySet) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Process other kinds of BioAssaySet that are neither experiment nor subset.

promptConfirmationOrAbort(String) - Method in class ubic.gemma.cli.util.AbstractCLI

Prompt the user for a confirmation or raise an exception to abort the AbstractCLI.doWork() method.

PROTOCOL - ubic.gemma.cli.completion.CompletionType

ProtocolAdderCli - Class in ubic.gemma.apps

ProtocolAdderCli() - Constructor for class ubic.gemma.apps.ProtocolAdderCli

ProtocolDeleterCli - Class in ubic.gemma.apps

ProtocolDeleterCli() - Constructor for class ubic.gemma.apps.ProtocolDeleterCli

ProtocolListCli - Class in ubic.gemma.apps

ProtocolListCli() - Constructor for class ubic.gemma.apps.ProtocolListCli

PrototypeScopeResolver - Class in ubic.gemma.cli.util

PrototypeScopeResolver() - Constructor for class ubic.gemma.cli.util.PrototypeScopeResolver

PubMedLoaderCli - Class in ubic.gemma.apps

Load PubMed files from XML files -- not used routinely!

PubMedLoaderCli() - Constructor for class ubic.gemma.apps.PubMedLoaderCli

PubMedSearcher - Class in ubic.gemma.apps

Simple application to perform pubmed searches from a list of terms, and persist the results in the database.

PubMedSearcher() - Constructor for class ubic.gemma.apps.PubMedSearcher

Q

quantitationTypeService - Variable in class ubic.gemma.apps.DetectQuantitationTypeCli

quoteIfNecessary(String) - Static method in class ubic.gemma.cli.util.ShellUtils

R

RawDataDeleterCli - Class in ubic.gemma.apps

RawDataDeleterCli() - Constructor for class ubic.gemma.apps.RawDataDeleterCli

RawExpressionDataWriterCli - Class in ubic.gemma.apps

RawExpressionDataWriterCli() - Constructor for class ubic.gemma.apps.RawExpressionDataWriterCli

readChangelogEntryFromConsole(ExpressionExperiment, String) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Read a changelog entry from the console.

readListFileToStrings(String) - Static method in class ubic.gemma.cli.util.FileUtils

may be tab-delimited, only first column used, commented (#) lines are ignored.

readListFileToStrings(Path) - Static method in class ubic.gemma.cli.util.FileUtils

RefreshExperimentCli - Class in ubic.gemma.apps

RefreshExperimentCli() - Constructor for class ubic.gemma.apps.RefreshExperimentCli

refreshExpressionExperimentFromGemmaWeb(ExpressionExperiment, boolean, boolean) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Refresh a dataset for Gemma Web.

ReplaceDataCli - Class in ubic.gemma.apps

Replace data in an existing data set.

ReplaceDataCli() - Constructor for class ubic.gemma.apps.ReplaceDataCli

reportProgress() - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

requires(Predicate<CommandLine>) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that the given predicate is satisfied.

resolveScopeMetadata(BeanDefinition) - Method in class ubic.gemma.cli.util.PrototypeScopeResolver

RNASeqBatchInfoCli - Class in ubic.gemma.apps

Deprecated.

this should not be necessary and the regular batch population tool can be used instead.

RNASeqBatchInfoCli() - Constructor for class ubic.gemma.apps.RNASeqBatchInfoCli

Deprecated.

RNASeqDataAddCli - Class in ubic.gemma.apps

Designed to add count and/or RPKM data to a data set that has only meta-data.

RNASeqDataAddCli() - Constructor for class ubic.gemma.apps.RNASeqDataAddCli

S

setAbortOnError() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Set this to stop processing experiments if an error occurs.

setAllowPositionalArguments() - Method in class ubic.gemma.cli.util.AbstractCLI

Allow positional arguments to be specified.

setApplicationContext(ApplicationContext) - Method in class ubic.gemma.cli.metrics.MeterRegistryCliConfigurer

setApplicationContext(ApplicationContext) - Method in class ubic.gemma.cli.util.AbstractCLI

setAuthentication(Authentication) - Method in interface ubic.gemma.cli.authentication.CLIAuthenticationAware

setAuthentication(Authentication) - Method in class ubic.gemma.cli.authentication.GemmaRestApiClientAuthenticator

setDefaultToAll() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Default to all datasets if no options are provided.

setEnvironment(Environment) - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

setEstimatedMaxTasks(int) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Set the maximum number of tasks that are expected to be run.

setEstimatedMaxTasks(int) - Method in class ubic.gemma.cli.util.AbstractCLI

Set the estimated maximum number of batch tasks to be processed.

setForce() - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Enable the forcing mode.

setQuantitationTypeIdentifierRequired() - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

Makes it so that the quantitation type identifier is required.

setReportFrequencyMillis(int) - Method in class ubic.gemma.cli.batch.BatchTaskProgressReporter

Set the frequency at which to report progress in milliseconds.

setReportFrequencyMillis(int) - Method in class ubic.gemma.cli.util.AbstractCLI

Set the frequency at which the batch task executor should report progress.

setRequireLogin() - Method in class ubic.gemma.cli.util.AbstractAuthenticatedCLI

Indicate that the command requires authentication.

setSingleExperimentMode() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Enable the single-experiment mode.

SettingsCompletionSource - Class in ubic.gemma.cli.completion

Provide completion for all available Gemma settings.

SettingsCompletionSource(boolean) - Constructor for class ubic.gemma.cli.completion.SettingsCompletionSource

setUsePreferredQuantitationType() - Method in class ubic.gemma.apps.ExpressionExperimentVectorsManipulatingCli

Use the preferred QT if no identifier is provided, otherwise process all the QTs.

setUseReferencesIfPossible() - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

Set this to allow reference to be retrieved instead of actual entities.

ShellUtils - Class in ubic.gemma.cli.util

ShellUtils() - Constructor for class ubic.gemma.cli.util.ShellUtils

shouldRun(Date, ArrayDesign, Class<? extends ArrayDesignAnalysisEvent>) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

shutdown() - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

shutdownNow() - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

SingleCellDataAggregateDeleterCli - Class in ubic.gemma.apps

SingleCellDataAggregateDeleterCli() - Constructor for class ubic.gemma.apps.SingleCellDataAggregateDeleterCli

SingleCellDataAggregatorCli - Class in ubic.gemma.apps

SingleCellDataAggregatorCli() - Constructor for class ubic.gemma.apps.SingleCellDataAggregatorCli

SingleCellDataDeleterCli - Class in ubic.gemma.apps

SingleCellDataDeleterCli() - Constructor for class ubic.gemma.apps.SingleCellDataDeleterCli

SingleCellDataDownloaderCli - Class in ubic.gemma.apps

SingleCellDataDownloaderCli() - Constructor for class ubic.gemma.apps.SingleCellDataDownloaderCli

SingleCellDataLoaderCli - Class in ubic.gemma.apps

SingleCellDataLoaderCli() - Constructor for class ubic.gemma.apps.SingleCellDataLoaderCli

SingleCellDataTransformCli - Class in ubic.gemma.apps

Transform various single-cell formats.

SingleCellDataTransformCli() - Constructor for class ubic.gemma.apps.SingleCellDataTransformCli

SingleCellDataWriterCli - Class in ubic.gemma.apps

SingleCellDataWriterCli() - Constructor for class ubic.gemma.apps.SingleCellDataWriterCli

singleCellExpressionExperimentService - Variable in class ubic.gemma.apps.DetectQuantitationTypeCli

SingleCellSparsityMetricsUpdaterCli - Class in ubic.gemma.apps

SingleCellSparsityMetricsUpdaterCli() - Constructor for class ubic.gemma.apps.SingleCellSparsityMetricsUpdaterCli

SplitExperimentCli - Class in ubic.gemma.apps

Split an experiment into parts based on an experimental factor

SplitExperimentCli() - Constructor for class ubic.gemma.apps.SplitExperimentCli

submit(Runnable) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

submit(Runnable, T) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

submit(Callable<T>) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

SUCCESS - Static variable in class ubic.gemma.cli.util.AbstractCLI

Exit code used for a successful AbstractCLI.doWork() execution.

SuppressBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch

SuppressBatchTaskSummaryWriter() - Constructor for class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter

SVDCli - Class in ubic.gemma.apps

SVDCli() - Constructor for class ubic.gemma.apps.SVDCli

SYSTEM - ubic.gemma.cli.util.CLI.CommandGroup

SystemCliContext - Class in ubic.gemma.cli.util

A context for the CLI based on System.

SystemCliContext(String, String[]) - Constructor for class ubic.gemma.cli.util.SystemCliContext

T

TAXON - ubic.gemma.cli.completion.CompletionType

TaxonLoaderCli - Class in ubic.gemma.apps

TaxonLoaderCli() - Constructor for class ubic.gemma.apps.TaxonLoaderCli

TextBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch

TextBatchTaskSummaryWriter(Appendable) - Constructor for class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter

toBatchObject(T) - Method in class ubic.gemma.cli.util.AbstractAutoSeekingCLI

Convert the given object to a serializable object for batch processing.

toBatchObject(ArrayDesign) - Method in class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

toBatchObject(BioAssaySet) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

toBatchObject(ExpressionExperiment) - Method in class ubic.gemma.apps.ExpressionExperimentManipulatingCLI

toBeSet(String) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that the given option is present.

toBeUnset(String) - Static method in class ubic.gemma.cli.util.OptionsUtils

Make sure that the given option is missing.

TsvBatchTaskSummaryWriter - Class in ubic.gemma.cli.batch

TsvBatchTaskSummaryWriter(Appendable) - Constructor for class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter

U

ubic.gemma.apps - package ubic.gemma.apps

This package contains built-in Gemma CLI applications.

ubic.gemma.cli.authentication - package ubic.gemma.cli.authentication

ubic.gemma.cli.batch - package ubic.gemma.cli.batch

Utilities for executing batch jobs via the CLI.

ubic.gemma.cli.completion - package ubic.gemma.cli.completion

This package provides completion support for the Gemma CLI.

ubic.gemma.cli.config - package ubic.gemma.cli.config

ubic.gemma.cli.logging - package ubic.gemma.cli.logging

ubic.gemma.cli.logging.log4j - package ubic.gemma.cli.logging.log4j

ubic.gemma.cli.main - package ubic.gemma.cli.main

ubic.gemma.cli.metrics - package ubic.gemma.cli.metrics

ubic.gemma.cli.util - package ubic.gemma.cli.util

ubic.gemma.contrib.apps - package ubic.gemma.contrib.apps

This package can be used by other Java packages to include CLIs.

UnifiedOntologyUpdaterCli - Class in ubic.gemma.apps

UnifiedOntologyUpdaterCli() - Constructor for class ubic.gemma.apps.UnifiedOntologyUpdaterCli

UpdateDatabaseCli - Class in ubic.gemma.apps

Update the database.

UpdateDatabaseCli() - Constructor for class ubic.gemma.apps.UpdateDatabaseCli

UpdateEe2AdCli - Class in ubic.gemma.apps

UpdateEe2AdCli() - Constructor for class ubic.gemma.apps.UpdateEe2AdCli

UpdateEE2CCli - Class in ubic.gemma.apps

UpdateEE2CCli() - Constructor for class ubic.gemma.apps.UpdateEE2CCli

UpdateGene2CsCli - Class in ubic.gemma.apps

UpdateGene2CsCli() - Constructor for class ubic.gemma.apps.UpdateGene2CsCli

UpdatePubMedCli - Class in ubic.gemma.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.apps.UpdatePubMedCli

V

valueOf(String) - Static method in enum ubic.gemma.cli.completion.CompletionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum ubic.gemma.cli.util.CLI.CommandGroup

Returns the enum constant of this type with the specified name.

values() - Static method in enum ubic.gemma.cli.completion.CompletionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum ubic.gemma.cli.util.CLI.CommandGroup

Returns an array containing the constants of this enum type, in the order they are declared.

VectorMergingCli - Class in ubic.gemma.apps

For experiments that used multiple array designs, merge the expression profiles

VectorMergingCli() - Constructor for class ubic.gemma.apps.VectorMergingCli

W

wrap(Runnable) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

wrap(Runnable) - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService

wrap(Callable<T>) - Method in class ubic.gemma.cli.batch.AbstractDelegatingExecutorService

wrap(Callable<T>) - Method in class ubic.gemma.cli.batch.BatchTaskExecutorService

write(BatchTaskProcessingResult) - Method in interface ubic.gemma.cli.batch.BatchTaskSummaryWriter

Write the result of a batch task.

write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.CompositeBatchTaskSummaryWriter

write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.LoggingBatchTaskSummaryWriter

write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.SuppressBatchTaskSummaryWriter

write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.TextBatchTaskSummaryWriter

write(BatchTaskProcessingResult) - Method in class ubic.gemma.cli.batch.TsvBatchTaskSummaryWriter

writeCompletions(CompletionSource, PrintStream) - Static method in class ubic.gemma.cli.completion.CompletionUtils

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