Package ubic.gemma.model.genome.gene

Class GeneValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<Gene>

ubic.gemma.model.genome.gene.GeneValueObject

All Implemented Interfaces:

Serializable, Identifiable

Direct Known Subclasses:

GeneEvidenceValueObject

public class GeneValueObject
extends IdentifiableValueObject<Gene>
implements Serializable

Author:

kelsey

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
GeneValueObject()	Required when using the class as a spring bean.
GeneValueObject(Long id)
GeneValueObject(Long geneId, String geneSymbol, String geneOfficialName, Taxon taxon)
GeneValueObject(Gene gene)
GeneValueObject(GeneValueObject otherBean)	Copies constructor from other GeneValueObject
GeneValueObject(Gene gene, boolean includeTaxon)

Method Summary

Modifier and Type	Method	Description
static GeneValueObject	convert2ValueObject(Gene gene)	Converts a Gene to a GeneValueObject
static Collection<GeneValueObject>	convertMembers2GeneValueObjects(Collection<GeneSetMember> setMembers)	A static method for easily converting GeneSetMembers into GeneValueObjects
String	getTaxonCommonName()
TaxonValueObject	getTaxonForGemmaRest()
Long	getTaxonId()
Long	getTaxonIdForGemmaRest()
String	getTaxonScientificName()
String	toString()

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

getId, setId

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneValueObject

public GeneValueObject()

Required when using the class as a spring bean.

GeneValueObject

public GeneValueObject(Long id)

GeneValueObject

public GeneValueObject(Gene gene)

Parameters:

gene - gene

GeneValueObject

public GeneValueObject(Gene gene,
                       boolean includeTaxon)

Parameters:

includeTaxon - include full taxon details in getTaxonForGemmaRest(), otherwise only getTaxonIdForGemmaRest() is filled

GeneValueObject

public GeneValueObject(GeneValueObject otherBean)

Copies constructor from other GeneValueObject

Parameters:

otherBean - , cannot be null

Throws:

NullPointerException - if the argument is null

GeneValueObject

public GeneValueObject(Long geneId,
                       String geneSymbol,
                       String geneOfficialName,
                       Taxon taxon)

Method Detail

convert2ValueObject

public static GeneValueObject convert2ValueObject(Gene gene)

Converts a Gene to a GeneValueObject

Parameters:

gene - a gene to be converted to a value object

Returns:

value object with the same basic characteristics as the given gene, including aliases.

convertMembers2GeneValueObjects

public static Collection<GeneValueObject> convertMembers2GeneValueObjects(Collection<GeneSetMember> setMembers)

A static method for easily converting GeneSetMembers into GeneValueObjects

Parameters:

setMembers - gene set members

Returns:

gene VOs

getTaxonId

public Long getTaxonId()

getTaxonForGemmaRest

public TaxonValueObject getTaxonForGemmaRest()

getTaxonIdForGemmaRest

public Long getTaxonIdForGemmaRest()

getTaxonCommonName

public String getTaxonCommonName()

getTaxonScientificName

public String getTaxonScientificName()

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<Gene>