Package ubic.gemma.model.expression.bioAssay

Class BioAssayValueObject

java.lang.Object

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

ubic.gemma.model.expression.bioAssay.BioAssayValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class BioAssayValueObject
extends IdentifiableValueObject<BioAssay>

Author:

Paul

See Also:

Serialized Form

Field Summary

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

id

Constructor Summary

Constructors

Constructor	Description
BioAssayValueObject()	Required when using the class as a spring bean.
BioAssayValueObject(Long id)
BioAssayValueObject(BioAssay bioAssay)
BioAssayValueObject(BioAssay bioAssay, boolean basic)
BioAssayValueObject(BioAssay bioAssay, boolean basic, boolean predictedOutlier)
BioAssayValueObject(BioAssay bioAssay, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, BioAssay sourceBioAssay, boolean basic, boolean allFactorValues)

Method Summary

Modifier and Type	Method	Description
static Collection<BioAssayValueObject>	convert2ValueObjects(Collection<BioAssay> bioAssays)
boolean	equals(Object obj)
DatabaseEntryValueObject	getAccession()
ArrayDesignValueObject	getArrayDesign()
String	getDescription()
String	getMetadata()
String	getName()
ArrayDesignValueObject	getOriginalPlatform()
Boolean	getPredictedOutlier()
Date	getProcessingDate()
BioMaterialValueObject	getSample()
Boolean	getSequencePairedReads()
Long	getSequenceReadCount()
Integer	getSequenceReadLength()
String	getShortName()
Long	getSourceBioAssayId()
Boolean	getUserFlaggedOutlier()
int	hashCode()
boolean	isOutlier()
void	setAccession(DatabaseEntryValueObject accession)
void	setArrayDesign(ArrayDesignValueObject arrayDesign)
void	setDescription(String description)
void	setMetadata(String metadata)
void	setName(String name)
void	setOriginalPlatform(ArrayDesignValueObject originalPlatform)
void	setOutlier(boolean outlier)
void	setPredictedOutlier(Boolean predictedOutlier)
void	setProcessingDate(Date processingDate)
void	setSample(BioMaterialValueObject sample)
void	setSequencePairedReads(Boolean sequencePairedReads)
void	setSequenceReadCount(Long sequenceReadCount)
void	setSequenceReadLength(Integer sequenceReadLength)
void	setShortName(String shortName)
void	setSourceBioAssayId(Long sourceBioAssayId)
void	setUserFlaggedOutlier(Boolean userFlaggedOutlier)
String	toString()

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

getId, setId

Methods inherited from class java.lang.Object

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

Constructor Detail

BioAssayValueObject

public BioAssayValueObject()

Required when using the class as a spring bean.

BioAssayValueObject

public BioAssayValueObject(BioAssay bioAssay)

BioAssayValueObject

public BioAssayValueObject(BioAssay bioAssay,
                           boolean basic)

BioAssayValueObject

public BioAssayValueObject(BioAssay bioAssay,
                           boolean basic,
                           boolean predictedOutlier)

BioAssayValueObject

public BioAssayValueObject(BioAssay bioAssay,
                           @Nullable
                           Map<ArrayDesign,ArrayDesignValueObject> ad2vo,
                           @Nullable
                           BioAssay sourceBioAssay,
                           boolean basic,
                           boolean allFactorValues)

Parameters:

ad2vo - pre-populated array design VOs by array design, or null to ignore and the VOs will be initialized via ArrayDesignValueObject(ArrayDesign)

sourceBioAssay - the source BioAssay if known, this corresponds to the assay of the source sample, but since there might be more than one, it must be picked explicitly based on the context

basic - if true, produce basic factor values in the corresponding biomaterial, see BioMaterialValueObject(BioMaterial, boolean, boolean) for more details

allFactorValues - include all FVs, including those inherited from the source biomaterial in the corresponding biomaterial

BioAssayValueObject

public BioAssayValueObject(Long id)

Method Detail

convert2ValueObjects

public static Collection<BioAssayValueObject> convert2ValueObjects(Collection<BioAssay> bioAssays)

getShortName

@Nullable
public String getShortName()

getSourceBioAssayId

public Long getSourceBioAssayId()

getAccession

public DatabaseEntryValueObject getAccession()

getArrayDesign

public ArrayDesignValueObject getArrayDesign()

getDescription

public String getDescription()

getMetadata

public String getMetadata()

getName

public String getName()

getOriginalPlatform

public ArrayDesignValueObject getOriginalPlatform()

getPredictedOutlier

public Boolean getPredictedOutlier()

getProcessingDate

public Date getProcessingDate()

getSample

public BioMaterialValueObject getSample()

getSequencePairedReads

public Boolean getSequencePairedReads()

getSequenceReadCount

public Long getSequenceReadCount()

getSequenceReadLength

public Integer getSequenceReadLength()

getUserFlaggedOutlier

public Boolean getUserFlaggedOutlier()

isOutlier

public boolean isOutlier()

setShortName

public void setShortName(@Nullable
                         String shortName)

setSourceBioAssayId

public void setSourceBioAssayId(Long sourceBioAssayId)

setAccession

public void setAccession(DatabaseEntryValueObject accession)

setArrayDesign

public void setArrayDesign(ArrayDesignValueObject arrayDesign)

setDescription

public void setDescription(String description)

setMetadata

public void setMetadata(String metadata)

setName

public void setName(String name)

setOriginalPlatform

public void setOriginalPlatform(ArrayDesignValueObject originalPlatform)

setOutlier

public void setOutlier(boolean outlier)

setPredictedOutlier

public void setPredictedOutlier(Boolean predictedOutlier)

setProcessingDate

public void setProcessingDate(Date processingDate)

setSample

public void setSample(BioMaterialValueObject sample)

setSequencePairedReads

public void setSequencePairedReads(Boolean sequencePairedReads)

setSequenceReadCount

public void setSequenceReadCount(Long sequenceReadCount)

setSequenceReadLength

public void setSequenceReadLength(Integer sequenceReadLength)

setUserFlaggedOutlier

public void setUserFlaggedOutlier(Boolean userFlaggedOutlier)

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<BioAssay>