Class ExpressionExperimentSubSet

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

ubic.gemma.model.analysis.Investigation

ubic.gemma.model.expression.experiment.BioAssaySet

ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet

All Implemented Interfaces:

Securable, SecuredChild, Auditable, Securable, SecuredChild<ExpressionExperiment>, Describable, Identifiable

@Entity
public class ExpressionExperimentSubSet
extends BioAssaySet
implements SecuredChild<ExpressionExperiment>

A subset of assays (or derived assays) from an ExpressionExperiment.

In the case of a "derived" assay, it is possible to walk up to the samples of the assays of the source experiment via BioMaterial.getSourceBioMaterial().

This is used for single-cell datasets to represent aggregated pseudo-bulks.

Author:

Paul

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	ExpressionExperimentSubSet.Factory

Field Summary

Fields

Modifier and Type	Field	Description
static final int	MAX_NAME_LENGTH	Maximum length of the name of a subset.
static final String	NAME_DELIMITER	Delimiter used to separate the source experiment name from the subset name.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Important note: The name should be compared in a case-insensitive manner.
Set<BioAssay>	getBioAssays()
ExpressionExperiment	getSecurityOwner()	Obtain the security owner of this secured child.
ExpressionExperiment	getSourceExperiment()
void	setBioAssays(Set<BioAssay> bioAssays)
void	setSourceExperiment(ExpressionExperiment sourceExperiment)

Methods inherited from class Investigation

getCharacteristics, getOtherRelevantPublications, getOwner, getPrimaryPublication, getSourceMetadata, getSourceMetadataSchemaVersion, getWorkflowState, getWorkflowStateEnteredAt, setCharacteristics, setOtherRelevantPublications, setOwner, setPrimaryPublication, setSourceMetadata, setSourceMetadataSchemaVersion, setWorkflowState, setWorkflowStateEnteredAt

Methods inherited from class AbstractAuditable

getAuditTrail, setAuditTrail

Methods inherited from class AbstractDescribable

getDescription, getName, hashCode, setDescription, setName, toString

Methods inherited from class AbstractIdentifiable

getId, setId

Methods inherited from class Object

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

Methods inherited from interface Identifiable

getId

Methods inherited from interface Securable

getId

Field Details

MAX_NAME_LENGTH

public static final int MAX_NAME_LENGTH

Maximum length of the name of a subset.

See Also:

• Constant Field Values

NAME_DELIMITER

public static final String NAME_DELIMITER

Delimiter used to separate the source experiment name from the subset name.

See Also:

• Constant Field Values

Constructor Details

ExpressionExperimentSubSet

public ExpressionExperimentSubSet()

No-arg constructor added to satisfy javabean contract

Method Details

getSourceExperiment

public ExpressionExperiment getSourceExperiment()

setSourceExperiment

public void setSourceExperiment(ExpressionExperiment sourceExperiment)

getBioAssays

public Set<BioAssay> getBioAssays()

Specified by:

getBioAssays in class BioAssaySet

setBioAssays

public void setBioAssays(Set<BioAssay> bioAssays)

Specified by:

setBioAssays in class BioAssaySet

getSecurityOwner

public ExpressionExperiment getSecurityOwner()

Description copied from interface: SecuredChild

Obtain the security owner of this secured child.

Secured children should always have an owner in the ACL table, but that relation is not always direct or mapped. A more robust way of checking is to look up the parent via AclObjectIdentity.getParentObject(). If the security owner cannot be determined, the implementation should define a setter so it can be temporarily assigned for creating the ACL identity.

Specified by:

getSecurityOwner in interface SecuredChild

Specified by:

getSecurityOwner in interface SecuredChild<ExpressionExperiment>

Returns:

the security owner, or null if not known.

equals

public boolean equals(Object object)

Description copied from class: AbstractDescribable

Important note: The name should be compared in a case-insensitive manner. You can use DescribableUtils.equalsByName(Describable, Describable) to get the correct behavior.

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 AbstractDescribable