Package ubic.gemma.apps
Class ArrayDesignProbeRenamerCli
java.lang.Object
ubic.gemma.cli.util.AbstractCLI
ubic.gemma.cli.util.AbstractAuthenticatedCLI
ubic.gemma.cli.util.AbstractAutoSeekingCLI<ArrayDesign>
ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
ubic.gemma.apps.ArrayDesignProbeRenamerCli
- All Implemented Interfaces:
org.springframework.beans.factory.Aware,org.springframework.beans.factory.InitializingBean,org.springframework.context.ApplicationContextAware,org.springframework.context.EnvironmentAware,CLI
Deprecated.
renaming probes is not a good idea in general
Put new names on probes. This is needed in some cases where probes were given generic names that weren't helpful for
matching them to sequences.
- Author:
- pavlidis
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Nested Class Summary
Nested classes/interfaces inherited from interface ubic.gemma.cli.util.CLI
CLI.CommandGroup -
Field Summary
Fields inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
arrayDesignReportService, arrayDesignService, auditEventService, auditTrailService, entityLocatorFields inherited from class ubic.gemma.cli.util.AbstractAutoSeekingCLI
FORCE_OPTIONFields inherited from class ubic.gemma.cli.util.AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidbuildArrayDesignOptions(org.apache.commons.cli.Options options) Deprecated.Deprecated.A short memorable name for the command that can be used to locate this class.protected voidprocessArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine) Deprecated.protected voidprocessArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess) Deprecated.Methods inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli
buildOptions, doAuthenticatedWork, getCommandGroup, getRelatedDesigns, isSubsumedOrMerged, needToRun, processArrayDesign, processOptions, shouldRun, toBatchObjectMethods inherited from class ubic.gemma.cli.util.AbstractAutoSeekingCLI
addAutoOption, addAutoOption, addErrorObject, addErrorObject, addErrorObject, addForceOption, addForceOption, addLimitingDateOption, addSuccessObject, addSuccessObject, addWarningObject, addWarningObject, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, noNeedToRun, setForceMethods inherited from class ubic.gemma.cli.util.AbstractAuthenticatedCLI
afterPropertiesSet, doWork, setAuthenticateAnonymously, setEnvironment, setRequireLoginMethods inherited from class ubic.gemma.cli.util.AbstractCLI
abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getApplicationContext, getBatchTaskExecutor, getBatchTaskProgressReporter, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getShortDesc, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis
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Constructor Details
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ArrayDesignProbeRenamerCli
public ArrayDesignProbeRenamerCli()Deprecated.
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Method Details
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getCommandName
Deprecated.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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buildArrayDesignOptions
protected void buildArrayDesignOptions(org.apache.commons.cli.Options options) Deprecated.- Overrides:
buildArrayDesignOptionsin classArrayDesignSequenceManipulatingCli
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processArrayDesignOptions
protected void processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine) Deprecated.- Overrides:
processArrayDesignOptionsin classArrayDesignSequenceManipulatingCli
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processArrayDesigns
Deprecated.- Overrides:
processArrayDesignsin classArrayDesignSequenceManipulatingCli
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