Package ubic.gemma.core.tasks.visualization

Class DifferentialExpressionGenesConditionsValueObject

java.lang.Object

ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject

All Implemented Interfaces:

Serializable

public class DifferentialExpressionGenesConditionsValueObject
extends Object
implements Serializable

Represents a complete set of data for a differential expression query over a set of genes x conditions (resultSets x contrasts).

Author:

anton

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	DifferentialExpressionGenesConditionsValueObject.Cell
class	DifferentialExpressionGenesConditionsValueObject.Condition	Represents one column in the differential expression view; one contrast in a resultset in an experiment.
class	DifferentialExpressionGenesConditionsValueObject.DiffExGene

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionGenesConditionsValueObject()

Method Summary

Modifier and Type	Method	Description
void	addBlackCell(Long geneId, String conditionId, double correctedPValue, double pValue, int numProbes, int numProbesDiffExpressed)
void	addCell(Long geneId, String conditionId, Double correctedPValue, Double foldChange, Integer numProbes, Integer numProbesDiffExpressed, Double uncorrectedPvalue)
void	addCondition(DifferentialExpressionGenesConditionsValueObject.Condition condition)	Initialize the column of cells for the given Condition, treating them as missing values.
void	addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene gene)
static String	constructConditionId(long resultSetId, long factorValueId)
Map<String,Map<Long,DifferentialExpressionGenesConditionsValueObject.Cell>>	getCellData()
List<DifferentialExpressionGenesConditionsValueObject.Condition>	getConditions()
List<DifferentialExpressionGenesConditionsValueObject.DiffExGene>	getGenes()
void	setAsNonSignficant(Long geneId, Long resultSetId)	Mark data as available, but not significant (so details will be missing).
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialExpressionGenesConditionsValueObject

public DifferentialExpressionGenesConditionsValueObject()

Method Detail

constructConditionId

public static String constructConditionId(long resultSetId,
                                          long factorValueId)

addBlackCell

public void addBlackCell(Long geneId,
                         String conditionId,
                         double correctedPValue,
                         double pValue,
                         int numProbes,
                         int numProbesDiffExpressed)

addCell

public void addCell(Long geneId,
                    String conditionId,
                    Double correctedPValue,
                    Double foldChange,
                    Integer numProbes,
                    Integer numProbesDiffExpressed,
                    Double uncorrectedPvalue)

addCondition

public void addCondition(DifferentialExpressionGenesConditionsValueObject.Condition condition)

Initialize the column of cells for the given Condition, treating them as missing values.

Parameters:

condition - condition

addGene

public void addGene(DifferentialExpressionGenesConditionsValueObject.DiffExGene gene)

getCellData

public Map<String,Map<Long,DifferentialExpressionGenesConditionsValueObject.Cell>> getCellData()

Returns:

Map of Condition IDs to map of Genes to the Cell holding the information for the results for that Gene x Condition combination.

setAsNonSignficant

public void setAsNonSignficant(Long geneId,
                               Long resultSetId)

Mark data as available, but not significant (so details will be missing). This is only used if we are not storing all the results. See bug 3365 for discussion.

Parameters:

geneId - gene id

resultSetId - result set id

getConditions

public List<DifferentialExpressionGenesConditionsValueObject.Condition> getConditions()

getGenes

public List<DifferentialExpressionGenesConditionsValueObject.DiffExGene> getGenes()

toString

public String toString()

Overrides:

toString in class Object