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

Class DifferentialExpressionAnalysisResultSetValueObject

java.lang.Object

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

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 ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet)	Create a simple analysis results set VO with limited data.
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet, boolean includeFactorValuesInContrasts, Map<Long,List<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()	Obtain the VO of the associated analysis result to this result set.
FactorValueBasicValueObject	getSecondBaselineGroup()
Set<TaxonValueObject>	getTaxa()
void	setAnalysis(DifferentialExpressionAnalysisValueObject analysis)
void	setBaselineGroup(FactorValueBasicValueObject baselineGroup)
void	setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)
void	setResults(Collection<DifferentialExpressionAnalysisResultValueObject> results)
void	setSecondBaselineGroup(FactorValueBasicValueObject secondBaselineGroup)
void	setTaxa(Set<TaxonValueObject> taxa)
String	toString()

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

Constructor Detail

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet)

Create a simple analysis results set VO with limited data.

DifferentialExpressionAnalysisResultSetValueObject

public DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet,
                                                          boolean includeFactorValuesInContrasts,
                                                          Map<Long,List<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 Detail

getAnalysis

public DifferentialExpressionAnalysisValueObject getAnalysis()

setAnalysis

public void setAnalysis(DifferentialExpressionAnalysisValueObject analysis)

getExperimentalFactors

public Collection<ExperimentalFactorValueObject> getExperimentalFactors()

setExperimentalFactors

public void setExperimentalFactors(Collection<ExperimentalFactorValueObject> experimentalFactors)

getBaselineGroup

@Nullable
public FactorValueBasicValueObject getBaselineGroup()

setBaselineGroup

public void setBaselineGroup(@Nullable
                             FactorValueBasicValueObject baselineGroup)

getSecondBaselineGroup

@Nullable
public FactorValueBasicValueObject getSecondBaselineGroup()

setSecondBaselineGroup

public void setSecondBaselineGroup(@Nullable
                                   FactorValueBasicValueObject secondBaselineGroup)

getTaxa

@Nullable
public Set<TaxonValueObject> getTaxa()

setTaxa

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

getResults

public Collection<DifferentialExpressionAnalysisResultValueObject> getResults()

Description copied from class: AnalysisResultSetValueObject

Obtain the VO of the associated analysis result to this result set.

Specified by:

getResults in class AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>

setResults

public void setResults(Collection<DifferentialExpressionAnalysisResultValueObject> results)

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<ExpressionAnalysisResultSet>