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)
void	setStandardized(boolean standardized)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

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 Details

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

setStandardized

public void setStandardized(boolean 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)