Package ubic.gemma.core.apps
Class AffyProbeCollapseCli
- java.lang.Object
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- ubic.gemma.core.util.AbstractCLI
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- ubic.gemma.core.util.AbstractAuthenticatedCLI
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- ubic.gemma.core.util.AbstractAutoSeekingCLI<ArrayDesign>
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- ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
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- ubic.gemma.core.apps.AffyProbeCollapseCli
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface ubic.gemma.core.util.CLI
CLI.CommandGroup
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Field Summary
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Fields inherited from class ubic.gemma.core.apps.ArrayDesignSequenceManipulatingCli
auditEventService, auditTrailService, entityLocator
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Fields inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI
FORCE_OPTION
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Fields inherited from class ubic.gemma.core.util.AbstractCLI
ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS
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Constructor Summary
Constructors Constructor Description AffyProbeCollapseCli()
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Method Summary
All Methods Instance Methods Concrete Methods 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
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Methods inherited from class ubic.gemma.core.util.AbstractAutoSeekingCLI
addAutoOption, addAutoOption, addForceOption, addLimitingDateOption, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, noNeedToRun, setForce
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Methods inherited from class ubic.gemma.core.util.AbstractAuthenticatedCLI
afterPropertiesSet, createBatchTaskExecutorService, doWork, setRequireLogin
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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
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Method Detail
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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 interfaceCLI
- Overrides:
getCommandName
in classAbstractCLI
- Returns:
- name; if null or blank, this will not be available as a shortcut command.
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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 interfaceCLI
- Overrides:
getShortDesc
in classAbstractCLI
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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 classArrayDesignSequenceManipulatingCli
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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 beforeAbstractCLI.doWork()
.- Overrides:
processOptions
in classArrayDesignSequenceManipulatingCli
- 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 ofAbstractCLI.FAILURE
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doAuthenticatedWork
protected void doAuthenticatedWork() throws IOException
- Specified by:
doAuthenticatedWork
in classAbstractAuthenticatedCLI
- Throws:
IOException
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