Package ubic.gemma.model.analysis.expression.diff

Class DifferentialExpressionAnalysisValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<DifferentialExpressionAnalysis>

ubic.gemma.model.analysis.AnalysisValueObject<DifferentialExpressionAnalysis>

ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class DifferentialExpressionAnalysisValueObject
extends AnalysisValueObject<DifferentialExpressionAnalysis>
implements Serializable

Summary of a differential expression analysis

Author:

paul

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_THRESHOLD

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisValueObject()
DifferentialExpressionAnalysisValueObject(DifferentialExpressionAnalysis analysis)	Does not populate the resultSets.

Method Summary

Modifier and Type	Method	Description
Collection<Long>	getArrayDesignsUsed()
Long	getBioAssaySetId()	Deprecated. use getExperimentAnalyzedId() instead
Long	getExperimentAnalyzedId()
Map<Long,Collection<FactorValueValueObject>>	getFactorValuesUsed()	Deprecated. This was renamed for clarity.
Map<Long,Collection<FactorValueValueObject>>	getFactorValuesUsedByExperimentalFactorId()	Produce a mapping of ExperimentalFactor IDs to FactorValue VOs used in this analysis.
Collection<DiffExResultSetSummaryValueObject>	getResultSets()
Long	getSourceExperiment()	Deprecated. use getSourceExperimentId() instead
Long	getSourceExperimentId()
ExperimentalFactorValueObject	getSubsetFactor()
Long	getSubsetFactorId()
FactorValueValueObject	getSubsetFactorValue()
Long	getSubsetFactorValueId()
boolean	isSubset()
void	setArrayDesignsUsed(Collection<Long> arrayDesignsUsed)
void	setExperimentAnalyzedId(Long experimentAnalyzedId)
void	setFactorValuesUsed(Map<Long,Collection<FactorValueValueObject>> factorValuesUsed)
void	setResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets)
void	setSourceExperimentId(Long sourceExperimentId)
void	setSubsetFactor(ExperimentalFactorValueObject subsetFactor)
void	setSubsetFactorId(Long subsetFactorId)
void	setSubsetFactorValue(FactorValueValueObject subsetFactorValue)
void	setSubsetFactorValueId(Long subsetFactorValueId)
String	toString()

Methods inherited from class ubic.gemma.model.analysis.AnalysisValueObject

getName, getProtocol, setName, setProtocol

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

canEqual, equals, getId, hashCode, setId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

DEFAULT_THRESHOLD

public static final double DEFAULT_THRESHOLD

See Also:

• Constant Field Values

Constructor Details

DifferentialExpressionAnalysisValueObject

public DifferentialExpressionAnalysisValueObject()

DifferentialExpressionAnalysisValueObject

public DifferentialExpressionAnalysisValueObject(DifferentialExpressionAnalysis analysis)

Does not populate the resultSets.

Parameters:

analysis - the analysis to read the values from

Method Details

getBioAssaySetId

@Deprecated
public Long getBioAssaySetId()

Deprecated.

use getExperimentAnalyzedId() instead

getSourceExperiment

@Deprecated
public Long getSourceExperiment()

Deprecated.

use getSourceExperimentId() instead

getFactorValuesUsed

@Deprecated
public Map<Long,Collection<FactorValueValueObject>> getFactorValuesUsed()

Deprecated.

This was renamed for clarity.

See Also:

• getFactorValuesUsedByExperimentalFactorId()

getFactorValuesUsedByExperimentalFactorId

public Map<Long,Collection<FactorValueValueObject>> getFactorValuesUsedByExperimentalFactorId()

Produce a mapping of ExperimentalFactor IDs to FactorValue VOs used in this analysis.

If this is a NOT a subset analysis, then this won't be important (so it may not be populated), but for subset analyses (subsetFactor != null), only the factor values present in the subset are relevant.

This can be null in certain cases if set to NULL via setFactorValuesUsed(Map) so that it does not appear in the JSON serialization, but you can assume it is non-null.

isSubset

public boolean isSubset()

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<DifferentialExpressionAnalysis>

getResultSets

public Collection<DiffExResultSetSummaryValueObject> getResultSets()

getArrayDesignsUsed

public Collection<Long> getArrayDesignsUsed()

getExperimentAnalyzedId

public Long getExperimentAnalyzedId()

getSourceExperimentId

public Long getSourceExperimentId()

getSubsetFactor

public ExperimentalFactorValueObject getSubsetFactor()

getSubsetFactorId

public Long getSubsetFactorId()

getSubsetFactorValue

public FactorValueValueObject getSubsetFactorValue()

getSubsetFactorValueId

public Long getSubsetFactorValueId()

setFactorValuesUsed

public void setFactorValuesUsed(Map<Long,Collection<FactorValueValueObject>> factorValuesUsed)

setResultSets

public void setResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets)

setArrayDesignsUsed

public void setArrayDesignsUsed(Collection<Long> arrayDesignsUsed)

setExperimentAnalyzedId

public void setExperimentAnalyzedId(Long experimentAnalyzedId)

setSourceExperimentId

public void setSourceExperimentId(Long sourceExperimentId)

setSubsetFactor

public void setSubsetFactor(ExperimentalFactorValueObject subsetFactor)

setSubsetFactorId

public void setSubsetFactorId(Long subsetFactorId)

setSubsetFactorValue

public void setSubsetFactorValue(FactorValueValueObject subsetFactorValue)

setSubsetFactorValueId

public void setSubsetFactorValueId(Long subsetFactorValueId)