Package ubic.gemma.model.genome.gene

Class GeneSet

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

ubic.gemma.model.genome.gene.GeneSet

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredNotChild, Auditable, Securable, SecuredNotChild, Describable, Identifiable

@Indexed
public class GeneSet
extends AbstractAuditable
implements SecuredNotChild

A grouping of genes that share a common relationship

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	GeneSet.Factory

Constructor Summary

Constructors

Constructor	Description
GeneSet()

Method Summary

Modifier and Type	Method	Description
static GeneSetMember	containsGene(Gene g, GeneSet gs)
boolean	equals(Object object)	Important note: Two objects with the same class and non-null ID must be considered equal.
Set<Characteristic>	getCharacteristics()
String	getDescription()	Obtain a human-readable description of the object
Long	getId()
Set<BibliographicReference>	getLiteratureSources()
Set<GeneSetMember>	getMembers()
String	getName()	Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
DatabaseEntry	getSourceAccession()
void	setCharacteristics(Set<Characteristic> characteristics)
void	setLiteratureSources(Set<BibliographicReference> literatureSources)
void	setMembers(Set<GeneSetMember> members)
void	setSourceAccession(DatabaseEntry sourceAccession)

Methods inherited from class ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

getAuditTrail, setAuditTrail

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

hashCode, setDescription, setName, 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 Details

GeneSet

public GeneSet()

Method Details

containsGene

public static GeneSetMember containsGene(Gene g,
 GeneSet gs)

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

getCharacteristics

@IndexedEmbedded
public Set<Characteristic> getCharacteristics()

setCharacteristics

public void setCharacteristics(Set<Characteristic> characteristics)

getLiteratureSources

@IndexedEmbedded
public Set<BibliographicReference> getLiteratureSources()

setLiteratureSources

public void setLiteratureSources(Set<BibliographicReference> literatureSources)

getMembers

@IndexedEmbedded
public Set<GeneSetMember> getMembers()

setMembers

public void setMembers(Set<GeneSetMember> members)

getSourceAccession

@IndexedEmbedded
public DatabaseEntry getSourceAccession()

setSourceAccession

public void setSourceAccession(DatabaseEntry sourceAccession)

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