Package ubic.gemma.model.genome

Class Gene

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.genome.ChromosomeFeature

ubic.gemma.model.genome.Gene

All Implemented Interfaces:

Serializable, Describable, Identifiable

@Indexed
public class Gene
extends ChromosomeFeature

Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Gene.Factory

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Returns true if the argument is an Describable instance and all identifiers for this entity equal the identifiers of the argument entity.
Set<DatabaseEntry>	getAccessions()
Set<GeneAlias>	getAliases()
String	getEnsemblId()
Long	getId()
Multifunctionality	getMultifunctionality()
String	getName()	Obtain the name of an object is a possibly ambiguous human-readable identifier that need not be an external database reference.
Integer	getNcbiGeneId()
String	getOfficialName()
String	getOfficialSymbol()
Set<PhenotypeAssociation>	getPhenotypeAssociations()	Deprecated.
Set<GeneProduct>	getProducts()
Taxon	getTaxon()
int	hashCode()	Returns a hash code based on this entity's identifiers.
void	setAccessions(Set<DatabaseEntry> accessions)
void	setAliases(Set<GeneAlias> aliases)
void	setEnsemblId(String ensemblId)
void	setMultifunctionality(Multifunctionality multifunctionality)
void	setNcbiGeneId(Integer ncbiGeneId)
void	setOfficialName(String officialName)
void	setOfficialSymbol(String officialSymbol)
void	setPhenotypeAssociations(Set<PhenotypeAssociation> phenotypeAssociations)	Deprecated.
void	setProducts(Set<GeneProduct> products)
void	setTaxon(Taxon taxon)
String	toString()

Methods inherited from class ubic.gemma.model.genome.ChromosomeFeature

getPhysicalLocation, getPreviousNcbiId, setPhysicalLocation, setPreviousNcbiId

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

getDescription, setDescription, setId, setName

Methods inherited from class java.lang.Object

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

Constructor Detail

Gene

public Gene()

No-arg constructor added to satisfy javabean contract

Method Detail

equals

public boolean equals(Object object)

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

hashCode

public int hashCode()

Description copied from class: AbstractDescribable

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

Overrides:

hashCode in class AbstractDescribable

toString

public String toString()

Overrides:

toString in class AbstractDescribable

See Also:

AbstractDescribable.toString()

getId

@DocumentId
public Long getId()

Specified by:

getId in interface Identifiable

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

getAccessions

@IndexedEmbedded
public Set<DatabaseEntry> getAccessions()

setAccessions

public void setAccessions(Set<DatabaseEntry> accessions)

getAliases

@IndexedEmbedded
public Set<GeneAlias> getAliases()

setAliases

public void setAliases(Set<GeneAlias> aliases)

getEnsemblId

@Field(analyze=NO)
public String getEnsemblId()

Returns:

An Ensembl ID for the gene.

setEnsemblId

public void setEnsemblId(String ensemblId)

getMultifunctionality

public Multifunctionality getMultifunctionality()

setMultifunctionality

public void setMultifunctionality(Multifunctionality multifunctionality)

getNcbiGeneId

@Field(analyze=NO)
public Integer getNcbiGeneId()

setNcbiGeneId

public void setNcbiGeneId(Integer ncbiGeneId)

getOfficialName

@Field(analyze=NO)
public String getOfficialName()

setOfficialName

public void setOfficialName(String officialName)

getOfficialSymbol

@Field(analyze=NO)
public String getOfficialSymbol()

setOfficialSymbol

public void setOfficialSymbol(String officialSymbol)

getPhenotypeAssociations

@Deprecated
public Set<PhenotypeAssociation> getPhenotypeAssociations()

Deprecated.

setPhenotypeAssociations

@Deprecated
public void setPhenotypeAssociations(Set<PhenotypeAssociation> phenotypeAssociations)

Deprecated.

getProducts

@IndexedEmbedded
public Set<GeneProduct> getProducts()

setProducts

public void setProducts(Set<GeneProduct> products)

getTaxon

@IndexedEmbedded
public Taxon getTaxon()

Returns:

Note that a Gene also has a chromosome, so the organism can be inferred that way as well. This direct association is a denormalization for queries that don't care about location, just species-membership.

setTaxon

public void setTaxon(Taxon taxon)