Class DiffExResultSetSummaryValueObject

java.lang.Object

ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject

All Implemented Interfaces:

Serializable

public class DiffExResultSetSummaryValueObject
extends Object
implements Serializable

Summary of a result set.

Author:

paul

See Also:

• DifferentialExpressionAnalysisValueObject
• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	DiffExResultSetSummaryValueObject.Prefetch	Pre-aggregated experimentalFactors + baselineGroup for a single ExpressionAnalysisResultSet, sourced from a batched join-fetch query so the VO ctor avoids three sequential lazy initializations.

Constructor Summary

Constructors

Constructor	Description
DiffExResultSetSummaryValueObject()
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet)
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet, ResultSetCountsValueObject counts)	Variant constructor that uses a pre-aggregated counts snapshot (cached) for the hit-list fields instead of walking ExpressionAnalysisResultSet.getHitListSizes().
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet, ResultSetCountsValueObject counts, DiffExResultSetSummaryValueObject.Prefetch prefetch)	Variant constructor that also accepts a DiffExResultSetSummaryValueObject.Prefetch snapshot of the result-set's experimentalFactors + baselineGroup associations gathered up-front by a batched HQL fetch in the caller.

Method Summary

Modifier and Type	Method	Description
protected boolean	canEqual(Object other)
boolean	equals(Object o)
Long	getAnalysisId()
Collection<Long>	getArrayDesignsUsed()
FactorValueValueObject	getBaselineGroup()
Collection<BioAssayValueObject>	getBioAssaysAnalyzed()	List of BioAssays analyzed
Long	getBioAssaySetAnalyzedId()	Analyzed BioAssaySet ID.
Integer	getDownregulatedCount()	Deprecated. use getNumberOfDownregulatedProbes() instead.
Collection<ExperimentalFactorValueObject>	getExperimentalFactors()
Collection<Long>	getFactorIds()
Long	getId()
Integer	getNumberOfDiffExpressedProbes()	Number of diffex probes in the Direction.EITHER hit list if available.
Integer	getNumberOfDownregulatedProbes()
Integer	getNumberOfGenesAnalyzed()
Integer	getNumberOfProbesAnalyzed()
Integer	getNumberOfUpregulatedProbes()
Double	getThreshold()	Threshold applied to the hitlist.
Integer	getUpregulatedCount()	Deprecated. use getNumberOfUpregulatedProbes() instead.
int	hashCode()
void	setAnalysisId(Long analysisId)
void	setArrayDesignsUsed(Collection<Long> arrayDesignsUsed)
void	setBaselineGroup(FactorValueValueObject baselineGroup)
void	setBioAssaysAnalyzed(Collection<BioAssayValueObject> bioAssaysAnalyzed)	List of BioAssays analyzed
void	setBioAssaySetAnalyzedId(Long bioAssaySetAnalyzedId)	Analyzed BioAssaySet ID.
void	setDownregulatedCount(Integer downregulatedCount)	Number of diffex probes in the Direction.DOWN hit list if available.
void	setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)
void	setFactorIds(Collection<Long> factorIds)
void	setId(Long id)
void	setNumberOfDiffExpressedProbes(Integer numberOfDiffExpressedProbes)	Number of diffex probes in the Direction.EITHER hit list if available.
void	setNumberOfGenesAnalyzed(Integer numberOfGenesAnalyzed)
void	setNumberOfProbesAnalyzed(Integer numberOfProbesAnalyzed)
void	setThreshold(Double threshold)	Threshold applied to the hitlist.
void	setUpregulatedCount(Integer upregulatedCount)	Number of diffex probes in the Direction.UP hit list if available.
String	toString()

Methods inherited from class Object

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

Constructor Details

DiffExResultSetSummaryValueObject

public DiffExResultSetSummaryValueObject()

DiffExResultSetSummaryValueObject

public DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet)

DiffExResultSetSummaryValueObject

public DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet,
 ResultSetCountsValueObject counts)

Variant constructor that uses a pre-aggregated counts snapshot (cached) for the hit-list fields instead of walking ExpressionAnalysisResultSet.getHitListSizes().

Used by the findByExperimentIds enrichment path so warm requests skip the collection initialization on the hitListSizes association.

DiffExResultSetSummaryValueObject

public DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet,
 @Nullable
 ResultSetCountsValueObject counts,
 @Nullable
 DiffExResultSetSummaryValueObject.Prefetch prefetch)

Variant constructor that also accepts a DiffExResultSetSummaryValueObject.Prefetch snapshot of the result-set's experimentalFactors + baselineGroup associations gathered up-front by a batched HQL fetch in the caller. When prefetch is non-null, the VO is populated without touching the lazy associations on resultSet, eliminating three round trips per RS in the findByExperimentIds hot path.

Passing null for prefetch preserves the original lazy-load behaviour.

Method Details

getUpregulatedCount

@Deprecated
public Integer getUpregulatedCount()

Deprecated.

use getNumberOfUpregulatedProbes() instead.

getNumberOfUpregulatedProbes

public Integer getNumberOfUpregulatedProbes()

getDownregulatedCount

@Deprecated
public Integer getDownregulatedCount()

Deprecated.

use getNumberOfDownregulatedProbes() instead.

getNumberOfDownregulatedProbes

public Integer getNumberOfDownregulatedProbes()

getId

public Long getId()

getAnalysisId

public Long getAnalysisId()

getArrayDesignsUsed

public Collection<Long> getArrayDesignsUsed()

getBaselineGroup

public FactorValueValueObject getBaselineGroup()

getExperimentalFactors

public Collection<ExperimentalFactorValueObject> getExperimentalFactors()

getFactorIds

public Collection<Long> getFactorIds()

getBioAssaySetAnalyzedId

public Long getBioAssaySetAnalyzedId()

Analyzed BioAssaySet ID.

This is redundant because of DifferentialExpressionAnalysisValueObject.getExperimentAnalyzedId(), and always displayed in that context in the RESTful API.

getBioAssaysAnalyzed

public Collection<BioAssayValueObject> getBioAssaysAnalyzed()

List of BioAssays analyzed

getNumberOfGenesAnalyzed

public Integer getNumberOfGenesAnalyzed()

getNumberOfProbesAnalyzed

public Integer getNumberOfProbesAnalyzed()

getThreshold

public Double getThreshold()

Threshold applied to the hitlist.

getNumberOfDiffExpressedProbes

public Integer getNumberOfDiffExpressedProbes()

Number of diffex probes in the Direction.EITHER hit list if available.

setId

public void setId(Long id)

setAnalysisId

public void setAnalysisId(Long analysisId)

setArrayDesignsUsed

public void setArrayDesignsUsed(Collection<Long> arrayDesignsUsed)

setBaselineGroup

public void setBaselineGroup(FactorValueValueObject baselineGroup)

setExperimentalFactors

public void setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)

setFactorIds

public void setFactorIds(Collection<Long> factorIds)

setBioAssaySetAnalyzedId

public void setBioAssaySetAnalyzedId(Long bioAssaySetAnalyzedId)

Analyzed BioAssaySet ID.

This is redundant because of DifferentialExpressionAnalysisValueObject.getExperimentAnalyzedId(), and always displayed in that context in the RESTful API.

setBioAssaysAnalyzed

public void setBioAssaysAnalyzed(Collection<BioAssayValueObject> bioAssaysAnalyzed)

List of BioAssays analyzed

setNumberOfGenesAnalyzed

public void setNumberOfGenesAnalyzed(Integer numberOfGenesAnalyzed)

setNumberOfProbesAnalyzed

public void setNumberOfProbesAnalyzed(Integer numberOfProbesAnalyzed)

setThreshold

public void setThreshold(Double threshold)

Threshold applied to the hitlist.

setNumberOfDiffExpressedProbes

public void setNumberOfDiffExpressedProbes(Integer numberOfDiffExpressedProbes)

Number of diffex probes in the Direction.EITHER hit list if available.

setUpregulatedCount

public void setUpregulatedCount(Integer upregulatedCount)

Number of diffex probes in the Direction.UP hit list if available.

setDownregulatedCount

public void setDownregulatedCount(Integer downregulatedCount)

Number of diffex probes in the Direction.DOWN hit list if available.

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

canEqual

protected boolean canEqual(Object other)

hashCode

public int hashCode()

Overrides:

hashCode in class Object