Package ubic.gemma.model.genome.gene

Class GeneProduct

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.genome.ChromosomeFeature

ubic.gemma.model.genome.gene.GeneProduct

All Implemented Interfaces:

Describable, Identifiable

@Indexed
public class GeneProduct
extends ChromosomeFeature

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GeneProduct.Factory

Constructor Summary

Constructors

Constructor	Description
GeneProduct()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Important note: Two objects with the same class and non-null ID must be considered equal.
Set<DatabaseEntry>	getAccessions()
Set<PhysicalLocation>	getExons()	Only used for transient instances in sequence analysis, we do not store exon locations in the database.
Gene	getGene()
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.
String	getNcbiGi()
String	getPreviousNcbiId()
int	hashCode()	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
boolean	isDummy()
void	setAccessions(Set<DatabaseEntry> accessions)
void	setDummy(boolean dummy)
void	setExons(Set<PhysicalLocation> exons)	Only used for transient instances, we do not store exon locations in the database.
void	setGene(Gene gene)
void	setNcbiGi(String ncbiGi)
String	toString()

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

getPhysicalLocation, setPhysicalLocation, setPreviousNcbiId

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

getDescription, 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

GeneProduct

public GeneProduct()

Method Detail

hashCode

public int hashCode()

Description copied from class: AbstractIdentifiable

Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.

Overrides:

hashCode in class AbstractDescribable

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

toString

public String toString()

Overrides:

toString in class AbstractDescribable

getId

@DocumentId
public Long getId()

Specified by:

getId in interface Identifiable

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

getAccessions

@IndexedEmbedded
public Set<DatabaseEntry> getAccessions()

setAccessions

public void setAccessions(Set<DatabaseEntry> accessions)

getExons

public Set<PhysicalLocation> getExons()

Only used for transient instances in sequence analysis, we do not store exon locations in the database.

Returns:

physical locations of exons

setExons

public void setExons(Set<PhysicalLocation> exons)

Only used for transient instances, we do not store exon locations in the database.

Parameters:

exons - new physical locations of exons

getGene

public Gene getGene()

setGene

public void setGene(Gene gene)

getNcbiGi

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

Returns:

GI for the gene product (if available)

setNcbiGi

public void setNcbiGi(String ncbiGi)

getPreviousNcbiId

@Field
public String getPreviousNcbiId()

Overrides:

getPreviousNcbiId in class ChromosomeFeature

Returns:

The last-used NCBI id for this feature, according to the history information provided by NCBI. This may be empty.

isDummy

public boolean isDummy()

setDummy

public void setDummy(boolean dummy)