Package ubic.gemma.model.expression.experiment

Class ExperimentalFactor

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.expression.experiment.ExperimentalFactor

All Implemented Interfaces:

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

@Indexed
public class ExperimentalFactor
extends AbstractDescribable
implements gemma.gsec.model.SecuredChild, Serializable

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

Author:

Paul

See Also:

Serialized Form

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)	Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
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.
gemma.gsec.model.Securable	getSecurityOwner()
FactorType	getType()
int	hashCode()	Returns a hash code based on this entity's identifiers.
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)

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

setDescription, setId, setName, toString

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

hashCode

public int hashCode()

Description copied from class: AbstractDescribable

Returns a hash code based on this entity's identifiers.

Overrides:

hashCode in class AbstractDescribable

equals

public boolean equals(Object obj)

Description copied from class: AbstractDescribable

Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

Overrides:

equals in class AbstractDescribable

getId

@DocumentId
public Long getId()

Specified by:

getId in interface Identifiable

Specified by:

getId in interface gemma.gsec.model.Securable

Overrides:

getId in class AbstractDescribable

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 gemma.gsec.model.Securable getSecurityOwner()

Specified by:

getSecurityOwner in interface gemma.gsec.model.SecuredChild

setSecurityOwner

public void setSecurityOwner(ExpressionExperiment securityOwner)

Parameters:

securityOwner - Used to hint the security system about who 'owns' this,

getAnnotations

@Deprecated
public Set<Characteristic> getAnnotations()

Deprecated.

setAnnotations

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

Deprecated.

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)

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)