Class ArrayDesignRepeatScanCli

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.ArrayDesignRepeatScanCli

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI

public class ArrayDesignRepeatScanCli
extends ArrayDesignSequenceManipulatingCli

Runs repeatmasker on array designs.

Author:

pavlidis

Nested Class Summary

Nested classes/interfaces inherited from interface CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ArrayDesignSequenceManipulatingCli

arrayDesignReportService, arrayDesignService, auditEventService, auditTrailService, entityLocator, MARK_ONLY_OPTION

Fields inherited from class AbstractAutoSeekingCLI

FORCE_OPTION

Fields inherited from class AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
ArrayDesignRepeatScanCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildArrayDesignOptions(org.apache.commons.cli.Options options)
String	getCommandName()	A short memorable name for the command that can be used to locate this class.
String	getShortDesc()	Obtain a short description for this command explaining what it does.
protected void	processArrayDesign(ArrayDesign design)
protected void	processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)
protected void	processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected boolean	selectsOwnPlatforms()	Whether the options of this CLI select platforms by some means other than -a, -f or -all.

Methods inherited from class ArrayDesignSequenceManipulatingCli

buildOptions, doAuthenticatedWork, getCommandGroup, getMarkOnlyReason, getRelatedDesigns, isSubsumedOrMerged, needToRun, processOptions, setExplicitADsOnly, shouldRun, toBatchObject

Methods inherited from class AbstractAutoSeekingCLI

addAutoOption, addAutoOption, addErrorObject, addErrorObject, addErrorObject, addForceOption, addForceOption, addLimitingDateOption, addSuccessObject, addSuccessObject, addWarningObject, addWarningObject, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, noNeedToRun, setForce

Methods inherited from class AbstractAuthenticatedCLI

afterPropertiesSet, doWork, setAuthenticateAnonymously, setEnvironment, setRequireLogin

Methods inherited from class AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, checkStandardOutput, executeCommand, getApplicationContext, getBatchTaskExecutor, getBatchTaskProgressReporter, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getPipelineJobReporter, getUsage, openStandardOutput, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ArrayDesignRepeatScanCli

public ArrayDesignRepeatScanCli()

Method Details

buildArrayDesignOptions

protected void buildArrayDesignOptions(org.apache.commons.cli.Options options)

Overrides:

buildArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

processArrayDesignOptions

protected void processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)
                                  throws org.apache.commons.cli.ParseException

Overrides:

processArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException

getCommandName

public String getCommandName()

Description copied from interface: CLI

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

Specified by:

getCommandName in interface CLI

Overrides:

getCommandName in class AbstractCLI

Returns:

name; if null or blank, this will not be available as a shortcut command.

processArrayDesigns

protected void processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)

Overrides:

processArrayDesigns in class ArrayDesignSequenceManipulatingCli

selectsOwnPlatforms

protected boolean selectsOwnPlatforms()

Description copied from class: ArrayDesignSequenceManipulatingCli

Whether the options of this CLI select platforms by some means other than -a, -f or -all.

If so, an empty selection from those options is not an error: ArrayDesignSequenceManipulatingCli.processArrayDesigns(Collection) is invoked with an empty collection and is responsible for finding its own platforms.

Overrides:

selectsOwnPlatforms in class ArrayDesignSequenceManipulatingCli

getShortDesc

public String getShortDesc()

Description copied from interface: CLI

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

Specified by:

getShortDesc in interface CLI

Overrides:

getShortDesc in class AbstractCLI

processArrayDesign

protected void processArrayDesign(ArrayDesign design)

Overrides:

processArrayDesign in class ArrayDesignSequenceManipulatingCli