Package ubic.gemma.web.controller.visualization

Class GeneExpressionProfile

java.lang.Object

ubic.gemma.web.controller.visualization.GeneExpressionProfile

public class GeneExpressionProfile
extends Object

Expression data for one probe; designed for conveying small amounts of data to clients. NOTE the data are standardized by default.

Author:

kelsey

Constructor Summary

Constructors

Constructor	Description
GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector)
GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector, Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes)
GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector, Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes, String color, Integer factor, Double pValue)
GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector, Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes, String color, Integer factor, Double pValue, boolean standardize)

Method Summary

Modifier and Type	Method	Description
String	getColor()
Integer	getFactor()
Collection<ubic.gemma.model.genome.gene.GeneValueObject>	getGenes()
ubic.gemma.model.expression.designElement.CompositeSequenceValueObject	getProbe()
double[]	getProfile()
Double	getPValue()
Double	getRank()
boolean	isAllMissing()
boolean	isStandardized()
void	setColor(String color)
void	setFactor(Integer factor)
void	setGenes(Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes)
void	setProbe(ubic.gemma.model.expression.designElement.CompositeSequenceValueObject probe)
void	setProfile(double[] profile)
void	setPValue(Double value)
void	setRank(Double rank)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneExpressionProfile

public GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector)

GeneExpressionProfile

public GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector,
                             Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes)

GeneExpressionProfile

public GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector,
                             Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes,
                             String color,
                             Integer factor,
                             Double pValue)

GeneExpressionProfile

public GeneExpressionProfile(ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject vector,
                             Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes,
                             String color,
                             Integer factor,
                             Double pValue,
                             boolean standardize)

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getColor

public String getColor()

getFactor

public Integer getFactor()

getGenes

public Collection<ubic.gemma.model.genome.gene.GeneValueObject> getGenes()

getProbe

public ubic.gemma.model.expression.designElement.CompositeSequenceValueObject getProbe()

getProfile

public double[] getProfile()

Returns:

the profile

getPValue

public Double getPValue()

getRank

public Double getRank()

isAllMissing

public boolean isAllMissing()

Returns:

the allMissing

isStandardized

public boolean isStandardized()

Returns:

the standardized

setColor

public void setColor(String color)

setFactor

public void setFactor(Integer factor)

setGenes

public void setGenes(Collection<ubic.gemma.model.genome.gene.GeneValueObject> genes)

setProbe

public void setProbe(ubic.gemma.model.expression.designElement.CompositeSequenceValueObject probe)

setProfile

public void setProfile(double[] profile)

Parameters:

profile - the profile to set

setPValue

public void setPValue(Double value)

setRank

public void setRank(Double rank)