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
Long	getBioAssaySetId()	Deprecated. use invalid reference #getExperimentAnalyzedId() instead
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.
Long	getSourceExperiment()	Deprecated. use invalid reference #getSourceExperimentId() instead
boolean	isSubset()
String	toString()

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

getName, getProtocol, setName, setProtocol

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

getId, setId

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, 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

invalid reference

#getExperimentAnalyzedId()

instead

getSourceExperiment

@Deprecated
public Long getSourceExperiment()

Deprecated.

use

invalid reference

#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

invalid reference

#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>