Class VectorMergingCli
- All Implemented Interfaces:
org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI
For experiments that used multiple array designs, merge the expression profiles
- Author:
- pavlidis
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Nested Class Summary
Nested classes/interfaces inherited from class ExpressionExperimentManipulatingCLI
ExpressionExperimentManipulatingCLI.ExpressionDataFileResultNested classes/interfaces inherited from interface CLI
CLI.CommandGroup -
Field Summary
Fields inherited from class ExpressionExperimentManipulatingCLI
auditEventService, auditTrailService, eeService, entityLocator, entityUrlBuilder, OUTPUT_DIR_OPTION, OUTPUT_FILE_OPTION, STANDARD_LOCATION_OPTION, STANDARD_OUTPUT_OPTIONFields inherited from class AbstractAutoSeekingCLI
FORCE_OPTIONFields inherited from class AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidbuildExperimentOptions(org.apache.commons.cli.Options options) A short memorable name for the command that can be used to locate this class.Obtain a short description for this command explaining what it does.protected voidprocessExpressionExperiment(ExpressionExperiment expressionExperiment) Process anExpressionExperiment.Methods inherited from class ExpressionExperimentManipulatingCLI
addExpressionDataFileOptions, addSingleExperimentOption, addSingleExperimentOption, buildOptions, doAuthenticatedWork, formatExperiment, getCommandGroup, getExpressionDataFileResult, isAbortOnError, noNeedToRun, preprocessExpressionExperiments, processExperimentOptions, processExpressionExperiments, processOptions, readChangelogEntryFromConsole, refreshExpressionExperimentFromGemmaWeb, setAbortOnError, setDefaultToAll, setSingleExperimentMode, setUseReferencesIfPossible, toBatchObjectMethods inherited from class AbstractAutoSeekingCLI
addAutoOption, addAutoOption, addErrorObject, addErrorObject, addErrorObject, addForceOption, addForceOption, addLimitingDateOption, addSuccessObject, addSuccessObject, addWarningObject, addWarningObject, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, setForceMethods inherited from class AbstractAuthenticatedCLI
afterPropertiesSet, doWork, setEnvironment, setRequireLoginMethods inherited from class AbstractCLI
abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getApplicationContext, getBatchTaskExecutor, getBatchTaskProgressReporter, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis
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Constructor Details
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VectorMergingCli
public VectorMergingCli()
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Method Details
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buildExperimentOptions
protected void buildExperimentOptions(org.apache.commons.cli.Options options) - Overrides:
buildExperimentOptionsin classExpressionExperimentManipulatingCLI
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getCommandName
Description copied from interface:CLIA short memorable name for the command that can be used to locate this class.- Specified by:
getCommandNamein interfaceCLI- Overrides:
getCommandNamein classAbstractCLI- Returns:
- name; if null or blank, this will not be available as a shortcut command.
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getShortDesc
Description copied from interface:CLIObtain a short description for this command explaining what it does.- Specified by:
getShortDescin interfaceCLI- Overrides:
getShortDescin classAbstractCLI
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processExpressionExperiment
Description copied from class:ExpressionExperimentManipulatingCLIProcess anExpressionExperiment.- Overrides:
processExpressionExperimentin classExpressionExperimentManipulatingCLI
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