Class DifferentialExpressionAnalysisResultSetValueObject

java.lang.Object

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

ubic.gemma.model.analysis.AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>

ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class DifferentialExpressionAnalysisResultSetValueObject
extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>

Wraps an ExpressionAnalysisResultSet and expose it to the public API.

See Also:

• Serialized Form

Field Summary

Fields inherited from class IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisResultSetValueObject()
DifferentialExpressionAnalysisResultSetValueObject(Long id)
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet)	Create a simple analysis results set VO with limited data.
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet, boolean includeFactorValuesInContrasts, Map<Long, Set<Gene>> result2Genes, boolean includeTaxonInGenes)	Create an expression analysis result set VO with all its associated results.

Method Summary

Modifier and Type	Method	Description
DifferentialExpressionAnalysisValueObject	getAnalysis()
FactorValueBasicValueObject	getBaselineGroup()
Collection<ExperimentalFactorValueObject>	getExperimentalFactors()
Collection<DifferentialExpressionAnalysisResultValueObject>	getResults()	Related analysis results.
FactorValueBasicValueObject	getSecondBaselineGroup()
Set<TaxonValueObject>	getTaxa()	When genes are included, this field is populated.
void	setAnalysis(DifferentialExpressionAnalysisValueObject analysis)
void	setBaselineGroup(FactorValueBasicValueObject baselineGroup)
void	setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)
void	setResults(Collection<DifferentialExpressionAnalysisResultValueObject> results)	Related analysis results.
void	setSecondBaselineGroup(FactorValueBasicValueObject secondBaselineGroup)
void	setTaxa(Set<TaxonValueObject> taxa)	When genes are included, this field is populated.
String	toString()

Methods inherited from class IdentifiableValueObject

canEqual, equals, getId, hashCode, setId

Methods inherited from class Object

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

Constructor Details

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject()

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject(Long id)

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet)

Create a simple analysis results set VO with limited data.

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet,
 boolean includeFactorValuesInContrasts,
 Map<Long, Set<Gene>> result2Genes,
 boolean includeTaxonInGenes)

Create an expression analysis result set VO with all its associated results.

Note: this constructor assumes that ExpressionAnalysisResultSet.getResults() has already been initialized.

Parameters:

includeFactorValuesInContrasts - include complete factorValue and secondFactorValue when serializing ContrastResultValueObject if true, else only the factorValueId and secondFactorValueId fields are populated. The latter approach is more compact and the full factors can be retrieved via experimentalFactors.

Method Details

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<ExpressionAnalysisResultSet>

getAnalysis

public DifferentialExpressionAnalysisValueObject getAnalysis()

getExperimentalFactors

public Collection<ExperimentalFactorValueObject> getExperimentalFactors()

getBaselineGroup

@Nullable
public FactorValueBasicValueObject getBaselineGroup()

getSecondBaselineGroup

@Nullable
public FactorValueBasicValueObject getSecondBaselineGroup()

getTaxa

@Nullable
public Set<TaxonValueObject> getTaxa()

When genes are included, this field is populated.

getResults

public Collection<DifferentialExpressionAnalysisResultValueObject> getResults()

Related analysis results.

Note that this field is excluded from the JSON serialization if left unset.

Specified by:

getResults in class AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>

setAnalysis

public void setAnalysis(DifferentialExpressionAnalysisValueObject analysis)

setExperimentalFactors

public void setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)

setBaselineGroup

public void setBaselineGroup(@Nullable
 FactorValueBasicValueObject baselineGroup)

setSecondBaselineGroup

public void setSecondBaselineGroup(@Nullable
 FactorValueBasicValueObject secondBaselineGroup)

setTaxa

public void setTaxa(@Nullable
 Set<TaxonValueObject> taxa)

When genes are included, this field is populated.

setResults

public void setResults(Collection<DifferentialExpressionAnalysisResultValueObject> results)

Related analysis results.

Note that this field is excluded from the JSON serialization if left unset.