Package ubic.gemma.core.apps

Class AffyProbeCollapseCli

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractAuthenticatedCLI

ubic.gemma.core.util.AbstractAutoSeekingCLI<ArrayDesign>

ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

ubic.gemma.core.apps.AffyProbeCollapseCli

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, CLI

public class AffyProbeCollapseCli
extends ArrayDesignSequenceManipulatingCli

Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences. This is what happens internally when we add sequences to a platform, but this makes it possible to see (and check) the sequences first before committing to them.

Should probably be in GemmaAnalysis but that is badly broken.

You just run this like

$GEMMACMD affyCollapse [filename]

It doesn't handle the regular argument setup, wasn't worth the trouble. Generates FASTA format but easy to change.

Author:

paul

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.util.CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

auditEventService, auditTrailService, entityLocator

Fields inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI

FORCE_OPTION

Fields inherited from class ubic.gemma.core.util.AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
AffyProbeCollapseCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doAuthenticatedWork()
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	processOptions(org.apache.commons.cli.CommandLine commandLine)	Process command line options.

Methods inherited from class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

getArrayDesignReportService, getArrayDesignService, getArrayDesignsToProcess, getCommandGroup, isSubsumedOrMerged, needToRun, shouldRun

Methods inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI

addAutoOption, addAutoOption, addForceOption, addLimitingDateOption, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, noNeedToRun, setForce

Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI

afterPropertiesSet, createBatchTaskExecutorService, doWork, setRequireLogin

Methods inherited from class ubic.gemma.core.util.AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getBatchTaskExecutor, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments

Methods inherited from class java.lang.Object

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

Constructor Detail

AffyProbeCollapseCli

public AffyProbeCollapseCli()

Method Detail

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.

getShortDesc

@Nullable
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

buildOptions

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

Description copied from class: AbstractCLI

Build option implementation.

Implement this method to add options to your command line, using the OptionBuilder.

This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

Overrides:

buildOptions in class ArrayDesignSequenceManipulatingCli

processOptions

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

Description copied from class: AbstractCLI

Process command line options.

Implement this to provide processing of options. It is called after AbstractCLI.buildOptions(Options) and right before AbstractCLI.doWork().

Overrides:

processOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.

doAuthenticatedWork

protected void doAuthenticatedWork()
                            throws IOException

Specified by:

doAuthenticatedWork in class AbstractAuthenticatedCLI

Throws:

IOException