Package ubic.gemma.core.apps

Class ArrayDesignBlatCli

java.lang.Object

ubic.gemma.core.util.AbstractCLI

ubic.gemma.core.util.AbstractSpringAwareCLI

ubic.gemma.core.util.AbstractCLIContextCLI

ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli

ubic.gemma.core.apps.ArrayDesignBlatCli

All Implemented Interfaces:

CLI

public class ArrayDesignBlatCli
extends ArrayDesignSequenceManipulatingCli

Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB. You must start the BLAT server first before using this.

Author:

pavlidis

Field Summary

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

auditEventService, auditTrailService

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

AUTO_OPTION_NAME, autoSeek, autoSeekEventType, FAILURE, FAILURE_FROM_ERROR_OBJECTS, FOOTER, HEADER, host, log, mDate, numThreads, port, SUCCESS, THREADS_OPTION

Constructor Summary

Constructors

Constructor	Description
ArrayDesignBlatCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doWork()	Command line implementation.
GemmaCLI.CommandGroup	getCommandGroup()	Obtain the command grup.
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, isSubsumedOrMerged, shouldRun

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

locateArrayDesign, readListFileToStrings, setTaxonByName

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

executeBatchTasks, getBean, getBean, getPersisterHelper, noNeedToRun, processStandardOptions, requireLogin

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

addAutoOption, addDateOption, addErrorObject, addErrorObject, addErrorObject, addHostAndPortOptions, addSuccessObject, addSuccessObject, addThreadsOption, buildStandardOptions, executeCommand, getDoubleOptionValue, getDoubleOptionValue, getFileNameOptionValue, getFileNameOptionValue, getIntegerOptionValue, getIntegerOptionValue, getLimitingDate, printHelp

Methods inherited from class java.lang.Object

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

Constructor Detail

ArrayDesignBlatCli

public ArrayDesignBlatCli()

Method Detail

getCommandGroup

public GemmaCLI.CommandGroup getCommandGroup()

Description copied from interface: CLI

Obtain the command grup.

Specified by:

getCommandGroup in interface CLI

Overrides:

getCommandGroup in class ArrayDesignSequenceManipulatingCli

Returns:

the command group for this CLI

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)

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

getCommandName

public String getCommandName()

Description copied from interface: CLI

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

Returns:

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

doWork

protected void doWork()
               throws Exception

Description copied from class: AbstractCLI

Command line implementation.

This is called after AbstractCLI.buildOptions(Options) and AbstractCLI.processOptions(CommandLine), so the implementation can assume that all its arguments have already been initialized.

Specified by:

doWork in class AbstractCLI

Throws:

Exception - in case of unrecoverable failure, an exception is thrown and will result in a AbstractCLI.FAILURE exit code, otherwise use AbstractCLI.addErrorObject(java.lang.Object, java.lang.String, java.lang.Throwable)

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 AbstractSpringAwareCLI