Package ubic.gemma.web.controller.visualization

Class VisualizationValueObject

java.lang.Object

ubic.gemma.web.controller.visualization.VisualizationValueObject

public class VisualizationValueObject
extends Object

Stores expression profile data from one expression experiment for plotting.

Author:

kelsey, paul

Constructor Summary

Constructors

Constructor	Description
VisualizationValueObject()
VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors, Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes, Double minPvalue, Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> validatedProbes)
VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors, List<ubic.gemma.model.genome.gene.GeneValueObject> genes, Collection<Long> validatedProbeList)
VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors, List<ubic.gemma.model.genome.gene.GeneValueObject> genes, Collection<Long> validatedProbeIdList, Double minPvalue)
VisualizationValueObject(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject dvvo)

Method Summary

Modifier and Type	Method	Description
ubic.gemma.model.expression.experiment.BioAssaySetValueObject	getEevo()
LinkedHashMap<String,LinkedHashMap<String,String>>	getFactorNames()
Collection<FactorProfile>	getFactorProfiles()
List<List<String>>	getFactorValues()
List<LinkedHashMap<String,String[]>>	getFactorValuesToNames()
Collection<GeneExpressionProfile>	getProfiles()
List<String>	getSampleNames()
void	setEevo(ubic.gemma.model.expression.experiment.BioAssaySetValueObject eevo)
void	setEEwithPvalue(ubic.gemma.model.expression.experiment.BioAssaySetValueObject ee, Double minP)
void	setFactorNames(LinkedHashMap<String,LinkedHashMap<String,String>> factorNames2)
void	setFactorProfiles(Collection<FactorProfile> factorProfiles)
void	setFactorValues(List<List<String>> factorValues)
void	setFactorValuesToNames(List<LinkedHashMap<String,String[]>> factorValueMaps2)
void	setProfiles(Collection<GeneExpressionProfile> profiles)
void	setSampleNames(List<String> sampleNames)
void	setUpFactorProfiles(LinkedHashMap<ubic.gemma.model.expression.bioAssay.BioAssayValueObject,LinkedHashMap<ubic.gemma.model.expression.experiment.ExperimentalFactor,Double>> layout)	Initialize the factor profiles.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

VisualizationValueObject

public VisualizationValueObject()

VisualizationValueObject

public VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors,
 Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes,
 Double minPvalue,
 Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> validatedProbes)

VisualizationValueObject

public VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors,
 List<ubic.gemma.model.genome.gene.GeneValueObject> genes,
 Collection<Long> validatedProbeList)

Parameters:

vectors - to be plotted (should come from a single expression experiment)

genes - Is list so that order is guaranteed. Need this so that colors are consistent.

validatedProbeList - Probes which are flagged as 'valid' in some sense. For example, in coexpression plots these are probes that provided the coexpression evidence, to differentiate them from the ones which are just being displayed because they assay the same gene.

Throws:

IllegalArgumentException - if vectors are mixed between EEs.

VisualizationValueObject

public VisualizationValueObject(Collection<ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject> vectors,
 List<ubic.gemma.model.genome.gene.GeneValueObject> genes,
 Collection<Long> validatedProbeIdList,
 Double minPvalue)

VisualizationValueObject

public VisualizationValueObject(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject dvvo)

Method Details

toString

public String toString()

Overrides:

toString in class Object

setUpFactorProfiles

public void setUpFactorProfiles(LinkedHashMap<ubic.gemma.model.expression.bioAssay.BioAssayValueObject,LinkedHashMap<ubic.gemma.model.expression.experiment.ExperimentalFactor,Double>> layout)

Initialize the factor profiles.

getEevo

public ubic.gemma.model.expression.experiment.BioAssaySetValueObject getEevo()

setEevo

public void setEevo(ubic.gemma.model.expression.experiment.BioAssaySetValueObject eevo)

getFactorNames

public LinkedHashMap<String,LinkedHashMap<String,String>> getFactorNames()

setFactorNames

public void setFactorNames(LinkedHashMap<String,LinkedHashMap<String,String>> factorNames2)

getFactorProfiles

public Collection<FactorProfile> getFactorProfiles()

setFactorProfiles

public void setFactorProfiles(Collection<FactorProfile> factorProfiles)

getFactorValues

public List<List<String>> getFactorValues()

setFactorValues

public void setFactorValues(List<List<String>> factorValues)

getFactorValuesToNames

public List<LinkedHashMap<String,String[]>> getFactorValuesToNames()

setFactorValuesToNames

public void setFactorValuesToNames(List<LinkedHashMap<String,String[]>> factorValueMaps2)

getProfiles

public Collection<GeneExpressionProfile> getProfiles()

setProfiles

public void setProfiles(Collection<GeneExpressionProfile> profiles)

getSampleNames

public List<String> getSampleNames()

setSampleNames

public void setSampleNames(List<String> sampleNames)

setEEwithPvalue

public void setEEwithPvalue(ubic.gemma.model.expression.experiment.BioAssaySetValueObject ee,
 Double minP)