Package ubic.gemma.model.expression.experiment

Class FactorValue

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.expression.experiment.FactorValue

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild, Identifiable

@Indexed
public class FactorValue
extends AbstractIdentifiable
implements SecuredChild

The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	FactorValue.Factory

Constructor Summary

Constructors

Constructor	Description
FactorValue()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Important note: Two objects with the same class and non-null ID must be considered equal.
Set<Statement>	getCharacteristics()	Collection of Statement describing this factor value.
ExperimentalFactor	getExperimentalFactor()
Long	getId()
Boolean	getIsBaseline()	Indicate if this factor value is a "forced" baseline or non-baseline condition.
Measurement	getMeasurement()	If this is a continuous factor, a measurement representing its value.
boolean	getNeedsAttention()	Indicate if this factor value needs attention.
Set<Characteristic>	getOldStyleCharacteristics()	Deprecated.
ExpressionExperiment	getSecurityOwner()
String	getValue()	Deprecated. use getMeasurement() or getCharacteristics() to retrieve the value.
int	hashCode()	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
void	setCharacteristics(Set<Statement> characteristics)
void	setExperimentalFactor(ExperimentalFactor experimentalFactor)
void	setIsBaseline(Boolean isBaseline)
void	setMeasurement(Measurement measurement)
void	setNeedsAttention(boolean troubled)
void	setOldStyleCharacteristics(Set<Characteristic> oldCharacteristics)	Deprecated.
void	setSecurityOwner(ExpressionExperiment ee)
void	setValue(String value)	Deprecated.
String	toString()

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

setId

Methods inherited from class java.lang.Object

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

Constructor Detail

FactorValue

public FactorValue()

Method Detail

getId

@DocumentId
public Long getId()

Specified by:

getId in interface Identifiable

Specified by:

getId in interface gemma.gsec.model.Securable

Overrides:

getId in class AbstractIdentifiable

getExperimentalFactor

public ExperimentalFactor getExperimentalFactor()

setExperimentalFactor

public void setExperimentalFactor(ExperimentalFactor experimentalFactor)

getIsBaseline

@Nullable
public Boolean getIsBaseline()

Indicate if this factor value is a "forced" baseline or non-baseline condition.

This is ignored if the factor is continuous.

setIsBaseline

public void setIsBaseline(@Nullable
                          Boolean isBaseline)

getValue

@Nullable
@Deprecated
public String getValue()

Deprecated.

use getMeasurement() or getCharacteristics() to retrieve the value.

setValue

@Deprecated
public void setValue(@Nullable
                     String value)

Deprecated.

getMeasurement

@Nullable
public Measurement getMeasurement()

If this is a continuous factor, a measurement representing its value.

setMeasurement

public void setMeasurement(@Nullable
                           Measurement measurement)

getCharacteristics

@IndexedEmbedded
public Set<Statement> getCharacteristics()

Collection of Statement describing this factor value.

setCharacteristics

public void setCharacteristics(Set<Statement> characteristics)

getOldStyleCharacteristics

@Deprecated
public Set<Characteristic> getOldStyleCharacteristics()

Deprecated.

Old-style characteristics from the 1.30 series.

This will be removed when all the characteristics are ported to the new style using Statement.

setOldStyleCharacteristics

@Deprecated
public void setOldStyleCharacteristics(Set<Characteristic> oldCharacteristics)

Deprecated.

getNeedsAttention

public boolean getNeedsAttention()

Indicate if this factor value needs attention.

If this is the case, there might be a FactorValueNeedsAttentionEvent event attached to the owning ExpressionExperiment with additional details.

setNeedsAttention

public void setNeedsAttention(boolean troubled)

getSecurityOwner

public ExpressionExperiment getSecurityOwner()

Specified by:

getSecurityOwner in interface gemma.gsec.model.SecuredChild

Specified by:

getSecurityOwner in interface SecuredChild

setSecurityOwner

public void setSecurityOwner(ExpressionExperiment ee)

hashCode

public int hashCode()

Description copied from class: AbstractIdentifiable

Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.

Specified by:

hashCode in class AbstractIdentifiable

equals

public boolean equals(Object object)

Description copied from class: AbstractIdentifiable

Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.

Specified by:

equals in class AbstractIdentifiable

toString

public String toString()

Overrides:

toString in class AbstractIdentifiable