Package ubic.gemma.model.expression.experiment

Class GeeqAdminValueObject

java.lang.Object

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

ubic.gemma.model.expression.experiment.GeeqValueObject

ubic.gemma.model.expression.experiment.GeeqAdminValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class GeeqAdminValueObject
extends GeeqValueObject

Represents administrative geeq information. On top of the classic VO, this one also exposes the underlying variables behind the public scores for suitability, quality, batch effect and batch confound.

Author:

paul, tesarst

See Also:

• Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
GeeqAdminValueObject()	Required when using the class as a spring bean
GeeqAdminValueObject(Geeq g)

Method Summary

Modifier and Type	Method	Description
double	getDetectedQualityScore()
double	getDetectedSuitabilityScore()
double	getManualQualityScore()
double	getManualSuitabilityScore()
String	getOtherIssues()
double	getQScoreBatchConfound()
double	getQScoreBatchEffect()
boolean	isManualBatchConfoundActive()
boolean	isManualBatchEffectActive()
boolean	isManualHasBatchConfound()
boolean	isManualHasNoBatchEffect()
boolean	isManualHasStrongBatchEffect()
boolean	isManualQualityOverride()
boolean	isManualSuitabilityOverride()
void	setDetectedQualityScore(double detectedQualityScore)
void	setDetectedSuitabilityScore(double detectedSuitabilityScore)
void	setManualBatchConfoundActive(boolean manualBatchConfoundActive)
void	setManualBatchEffectActive(boolean manualBatchEffectActive)
void	setManualHasBatchConfound(boolean manualHasBatchConfound)
void	setManualHasNoBatchEffect(boolean manualHasNoBatchEffect)
void	setManualHasStrongBatchEffect(boolean manualHasStrongBatchEffect)
void	setManualQualityOverride(boolean manualQualityOverride)
void	setManualQualityScore(double manualQualityScore)
void	setManualSuitabilityOverride(boolean manualSuitabilityOverride)
void	setManualSuitabilityScore(double manualSuitabilityScore)
void	setOtherIssues(String otherIssues)
void	setQScoreBatchConfound(double qScoreBatchConfound)
void	setQScoreBatchEffect(double qScoreBatchEffect)
String	toString()

Methods inherited from class ubic.gemma.model.expression.experiment.GeeqValueObject

getCorrMatIssues, getPublicQualityScore, getPublicSuitabilityScore, getqScoreBatchInfo, getqScoreOutliers, getqScorePlatformsTech, getqScorePublicBatchConfound, getqScorePublicBatchEffect, getqScoreReplicates, getqScoreSampleCorrelationVariance, getqScoreSampleMeanCorrelation, getqScoreSampleMedianCorrelation, getReplicatesIssues, getsScoreAvgPlatformPopularity, getsScoreAvgPlatformSize, getsScoreMissingValues, getsScorePlatformAmount, getsScorePlatformsTechMulti, getsScorePublication, getsScoreRawData, getsScoreSampleSize, isBatchCorrected, isNoVectors, setBatchCorrected, setCorrMatIssues, setNoVectors, setPublicQualityScore, setPublicSuitabilityScore, setQScoreBatchInfo, setQScoreOutliers, setQScorePlatformsTech, setQScorePublicBatchConfound, setQScorePublicBatchEffect, setQScoreReplicates, setQScoreSampleCorrelationVariance, setQScoreSampleMeanCorrelation, setQScoreSampleMedianCorrelation, setReplicatesIssues, setSScoreAvgPlatformPopularity, setSScoreAvgPlatformSize, setSScoreMissingValues, setSScorePlatformAmount, setSScorePlatformsTechMulti, setSScorePublication, setSScoreRawData, setSScoreSampleSize

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

canEqual, equals, getId, hashCode, setId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

GeeqAdminValueObject

public GeeqAdminValueObject()

Required when using the class as a spring bean

GeeqAdminValueObject

public GeeqAdminValueObject(Geeq g)

Method Details

getDetectedQualityScore

public double getDetectedQualityScore()

getManualQualityScore

public double getManualQualityScore()

isManualQualityOverride

public boolean isManualQualityOverride()

getDetectedSuitabilityScore

public double getDetectedSuitabilityScore()

getManualSuitabilityScore

public double getManualSuitabilityScore()

isManualSuitabilityOverride

public boolean isManualSuitabilityOverride()

getQScoreBatchEffect

public double getQScoreBatchEffect()

isManualHasStrongBatchEffect

public boolean isManualHasStrongBatchEffect()

isManualHasNoBatchEffect

public boolean isManualHasNoBatchEffect()

isManualBatchEffectActive

public boolean isManualBatchEffectActive()

getQScoreBatchConfound

public double getQScoreBatchConfound()

isManualHasBatchConfound

public boolean isManualHasBatchConfound()

isManualBatchConfoundActive

public boolean isManualBatchConfoundActive()

getOtherIssues

public String getOtherIssues()

setDetectedQualityScore

public void setDetectedQualityScore(double detectedQualityScore)

setManualQualityScore

public void setManualQualityScore(double manualQualityScore)

setManualQualityOverride

public void setManualQualityOverride(boolean manualQualityOverride)

setDetectedSuitabilityScore

public void setDetectedSuitabilityScore(double detectedSuitabilityScore)

setManualSuitabilityScore

public void setManualSuitabilityScore(double manualSuitabilityScore)

setManualSuitabilityOverride

public void setManualSuitabilityOverride(boolean manualSuitabilityOverride)

setQScoreBatchEffect

public void setQScoreBatchEffect(double qScoreBatchEffect)

setManualHasStrongBatchEffect

public void setManualHasStrongBatchEffect(boolean manualHasStrongBatchEffect)

setManualHasNoBatchEffect

public void setManualHasNoBatchEffect(boolean manualHasNoBatchEffect)

setManualBatchEffectActive

public void setManualBatchEffectActive(boolean manualBatchEffectActive)

setQScoreBatchConfound

public void setQScoreBatchConfound(double qScoreBatchConfound)

setManualHasBatchConfound

public void setManualHasBatchConfound(boolean manualHasBatchConfound)

setManualBatchConfoundActive

public void setManualBatchConfoundActive(boolean manualBatchConfoundActive)

setOtherIssues

public void setOtherIssues(String otherIssues)

toString

public String toString()

Overrides:

toString in class GeeqValueObject