Package ubic.gemma.model.expression.experiment

Class ExperimentalFactor

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.expression.experiment.ExperimentalFactor

All Implemented Interfaces:

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

@Indexed
public class ExperimentalFactor
extends AbstractDescribable
implements SecuredChild

ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).

Author:

Paul

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ExperimentalFactor.Factory

Constructor Summary

Constructors

Constructor	Description
ExperimentalFactor()	No-arg constructor added to satisfy javabean contract

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)	Important note: Two objects with the same class and non-null ID must be considered equal.
Set<Characteristic>	getAnnotations()	Deprecated.
Characteristic	getCategory()	Obtain the category of this experimental factor.
String	getDescription()	Obtain a human-readable description of the object
ExperimentalDesign	getExperimentalDesign()
Set<FactorValue>	getFactorValues()
Long	getId()
String	getName()	Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
Securable	getSecurityOwner()
FactorType	getType()
void	setAnnotations(Set<Characteristic> annotations)	Deprecated.
void	setCategory(Characteristic category)
void	setExperimentalDesign(ExperimentalDesign experimentalDesign)
void	setFactorValues(Set<FactorValue> factorValues)
void	setSecurityOwner(ExpressionExperiment securityOwner)
void	setType(FactorType type)
String	toString()

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

hashCode, setDescription, setName

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

ExperimentalFactor

public ExperimentalFactor()

No-arg constructor added to satisfy javabean contract

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

getName

@Field
public String getName()

Description copied from interface: Describable

Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.

Specified by:

getName in interface Describable

Overrides:

getName in class AbstractDescribable

getDescription

@Field(store=YES)
public String getDescription()

Description copied from interface: Describable

Obtain a human-readable description of the object

Specified by:

getDescription in interface Describable

Overrides:

getDescription in class AbstractDescribable

getSecurityOwner

public Securable getSecurityOwner()

Specified by:

getSecurityOwner in interface gemma.gsec.model.SecuredChild

Specified by:

getSecurityOwner in interface SecuredChild

setSecurityOwner

public void setSecurityOwner(ExpressionExperiment securityOwner)

getType

public FactorType getType()

Returns:

Categorical vs. continuous. Continuous factors must have a 'measurement' associated with the factorvalues, Categorical ones must not.

setType

public void setType(FactorType type)

getCategory

@Nullable
@IndexedEmbedded
public Characteristic getCategory()

Obtain the category of this experimental factor.

Returns:

the category or null if annotated automatically from GEO or used as a dummy.

setCategory

public void setCategory(@Nullable
                        Characteristic category)

getExperimentalDesign

public ExperimentalDesign getExperimentalDesign()

setExperimentalDesign

public void setExperimentalDesign(ExperimentalDesign experimentalDesign)

getFactorValues

@IndexedEmbedded
public Set<FactorValue> getFactorValues()

Returns:

The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor.

setFactorValues

public void setFactorValues(Set<FactorValue> factorValues)

getAnnotations

@Deprecated
public Set<Characteristic> getAnnotations()

Deprecated.

setAnnotations

@Deprecated
public void setAnnotations(Set<Characteristic> annotations)

Deprecated.

equals

public boolean equals(Object obj)

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 AbstractDescribable