Package ubic.gemma.core.tasks.analysis.diffex

Class DifferentialExpressionAnalysisTaskCommand

java.lang.Object

ubic.gemma.core.job.TaskCommand

ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

DifferentialExpressionAnalysisRemoveTaskCommand

public class DifferentialExpressionAnalysisTaskCommand
extends TaskCommand

A command object to be used by spaces.

Author:

keshav

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.core.job.TaskCommand

MAX_QUEUING_MILLIS, MAX_RUNTIME_MILLIS

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisTaskCommand(boolean forceAnalysis, ExpressionExperiment expressionExperiment)
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee)
DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee, DifferentialExpressionAnalysis toRedo)

Method Summary

Modifier and Type	Method	Description
AnalysisType	getAnalysisType()
ExpressionExperiment	getExpressionExperiment()
Collection<ExperimentalFactor>	getFactors()
ExperimentalFactor	getSubsetFactor()
Class<? extends Task<? extends TaskCommand>>	getTaskClass()	Obtain the class of the Task object that will be run for this command.
DifferentialExpressionAnalysis	getToRedo()
boolean	isForceAnalysis()
boolean	isIncludeInteractions()
boolean	isModerateStatistics()
boolean	isUseWeights()
void	setAnalysisType(AnalysisType analysisType)
void	setExpressionExperiment(ExpressionExperiment expressionExperiment)
void	setFactors(Collection<ExperimentalFactor> factors)
void	setForceAnalysis(boolean forceAnalysis)
void	setIncludeInteractions(boolean includeInteractions)
void	setModerateStatistics(boolean moderateStatistics)
void	setSubsetFactor(ExperimentalFactor subsetFactor)
void	setToRedo(DifferentialExpressionAnalysis toRedo)
void	setUseWeights(boolean useWeights)

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialExpressionAnalysisTaskCommand

public DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee)

DifferentialExpressionAnalysisTaskCommand

public DifferentialExpressionAnalysisTaskCommand(ExpressionExperiment ee,
                                                 DifferentialExpressionAnalysis toRedo)

DifferentialExpressionAnalysisTaskCommand

public DifferentialExpressionAnalysisTaskCommand(boolean forceAnalysis,
                                                 ExpressionExperiment expressionExperiment)

Method Detail

getAnalysisType

public AnalysisType getAnalysisType()

setAnalysisType

public void setAnalysisType(AnalysisType analysisType)

getExpressionExperiment

public ExpressionExperiment getExpressionExperiment()

setExpressionExperiment

public void setExpressionExperiment(ExpressionExperiment expressionExperiment)

getFactors

public Collection<ExperimentalFactor> getFactors()

setFactors

public void setFactors(Collection<ExperimentalFactor> factors)

getSubsetFactor

public ExperimentalFactor getSubsetFactor()

Returns:

the subsetFactor

setSubsetFactor

public void setSubsetFactor(ExperimentalFactor subsetFactor)

Parameters:

subsetFactor - the subsetFactor to set

getTaskClass

public Class<? extends Task<? extends TaskCommand>> getTaskClass()

Description copied from class: TaskCommand

Obtain the class of the Task object that will be run for this command.

If null, the task command cannot be submitted through TaskRunningService.submitTaskCommand(TaskCommand) and a task object must be explicitly created.

For now, this how we map from TaskCommand to Task that actually runs it. We have to have this mapping somewhere until we make Tasks themselves serializable. Tasks are not readily serializable because they have dependencies to Spring services. at which point TaskCommand can be deprecated(or remain as TaskContext).

Overrides:

getTaskClass in class TaskCommand

getToRedo

public DifferentialExpressionAnalysis getToRedo()

setToRedo

public void setToRedo(DifferentialExpressionAnalysis toRedo)

isForceAnalysis

public boolean isForceAnalysis()

setForceAnalysis

public void setForceAnalysis(boolean forceAnalysis)

isIncludeInteractions

public boolean isIncludeInteractions()

setIncludeInteractions

public void setIncludeInteractions(boolean includeInteractions)

Parameters:

includeInteractions - Sets preference for interactions to be included.

isModerateStatistics

public boolean isModerateStatistics()

setModerateStatistics

public void setModerateStatistics(boolean moderateStatistics)

isUseWeights

public boolean isUseWeights()

setUseWeights

public void setUseWeights(boolean useWeights)