Package ubic.gemma.model.genome.gene.phenotype.valueObject

Class EvidenceValueObject<E extends PhenotypeAssociation>

java.lang.Object

ubic.gemma.model.IdentifiableValueObject<E>

ubic.gemma.model.genome.gene.phenotype.valueObject.EvidenceValueObject<E>

All Implemented Interfaces:

Serializable, Comparable<EvidenceValueObject<E>>, Identifiable

Direct Known Subclasses:

DiffExpressionEvidenceValueObject, ExperimentalEvidenceValueObject, GenericEvidenceValueObject, LiteratureEvidenceValueObject

public class EvidenceValueObject<E extends PhenotypeAssociation>
extends IdentifiableValueObject<E>
implements Comparable<EvidenceValueObject<E>>, Serializable

Parent class of all evidence value objects

Author:

nicolas

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.IdentifiableValueObject

id

Constructor Summary

Constructors

Modifier	Constructor	Description
	EvidenceValueObject()	Required when using the class as a spring bean.
protected	EvidenceValueObject(E phenotypeAssociation)	set fields common to all evidence.
	EvidenceValueObject(Long id)
protected	EvidenceValueObject(Long id, Integer geneNCBI, Set<CharacteristicValueObject> phenotypes, String description, String evidenceCode, boolean isNegativeEvidence, EvidenceSourceValueObject evidenceSource)

Method Summary

Modifier and Type	Method	Description
int	compareTo(EvidenceValueObject<E> evidenceValueObject)
boolean	equals(Object obj)
PhenotypeMappingType	findPhenotypeMappingAsEnum()
String	getClassName()
String	getDescription()
String	getEvidenceCode()
EvidenceSecurityValueObject	getEvidenceSecurityValueObject()
EvidenceSourceValueObject	getEvidenceSource()
String	getExternalUrl()
Long	getGeneId()
Integer	getGeneNCBI()
String	getGeneOfficialName()
String	getGeneOfficialSymbol()
boolean	getIsNegativeEvidence()
Long	getLastUpdated()
String	getOriginalPhenotype()
Set<PhenotypeAssPubValueObject>	getPhenotypeAssPubVO()
String	getPhenotypeMapping()
Set<CharacteristicValueObject>	getPhenotypes()
Set<String>	getPhenotypesValueUri()
String	getRelationship()
ScoreValueObject	getScoreValueObject()
String	getTaxonCommonName()
int	hashCode()
boolean	isContainQueryPhenotype()
boolean	isHomologueEvidence()
void	setClassName(String className)
void	setContainQueryPhenotype(boolean containQueryPhenotype)
void	setDescription(String description)
void	setEvidenceCode(String evidenceCode)
void	setEvidenceSecurityValueObject(EvidenceSecurityValueObject evidenceSecurityValueObject)
void	setEvidenceSource(EvidenceSourceValueObject evidenceSource)
void	setGeneId(Long geneId)
void	setGeneNCBI(Integer geneNCBI)
void	setGeneOfficialName(String geneOfficialName)
void	setGeneOfficialSymbol(String geneOfficialSymbol)
void	setHomologueEvidence(boolean isHomologueEvidence)
void	setIsNegativeEvidence(boolean isNegativeEvidence)
void	setLastUpdated(Long lastUpdated)
void	setOriginalPhenotype(String originalPhenotype)
void	setPhenotypeAssPubVO(Set<PhenotypeAssPubValueObject> phenotypeAssPubVO)
void	setPhenotypeMapping(String phenotypeMapping)
void	setPhenotypes(Set<CharacteristicValueObject> phenotypes)
void	setRelationship(String relationship)
void	setScoreValueObject(ScoreValueObject scoreValueObject)
void	setTaxonCommonName(String taxonCommonName)
String	toString()

Methods inherited from class ubic.gemma.model.IdentifiableValueObject

getId, setId

Methods inherited from class java.lang.Object

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

Constructor Detail

EvidenceValueObject

public EvidenceValueObject()

Required when using the class as a spring bean.

EvidenceValueObject

public EvidenceValueObject(Long id)

EvidenceValueObject

protected EvidenceValueObject(Long id,
                              Integer geneNCBI,
                              Set<CharacteristicValueObject> phenotypes,
                              String description,
                              String evidenceCode,
                              boolean isNegativeEvidence,
                              EvidenceSourceValueObject evidenceSource)

EvidenceValueObject

protected EvidenceValueObject(E phenotypeAssociation)

set fields common to all evidence. Entity to Value Object

Parameters:

phenotypeAssociation - phenotype association

Method Detail

compareTo

public int compareTo(EvidenceValueObject<E> evidenceValueObject)

Specified by:

compareTo in interface Comparable<E extends PhenotypeAssociation>

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getClassName

public String getClassName()

setClassName

public void setClassName(String className)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getEvidenceCode

public String getEvidenceCode()

setEvidenceCode

public void setEvidenceCode(String evidenceCode)

getEvidenceSecurityValueObject

public EvidenceSecurityValueObject getEvidenceSecurityValueObject()

setEvidenceSecurityValueObject

public void setEvidenceSecurityValueObject(EvidenceSecurityValueObject evidenceSecurityValueObject)

getEvidenceSource

public EvidenceSourceValueObject getEvidenceSource()

setEvidenceSource

public void setEvidenceSource(EvidenceSourceValueObject evidenceSource)

getExternalUrl

public String getExternalUrl()

getGeneId

public Long getGeneId()

setGeneId

public void setGeneId(Long geneId)

getGeneNCBI

public Integer getGeneNCBI()

setGeneNCBI

public void setGeneNCBI(Integer geneNCBI)

getGeneOfficialName

public String getGeneOfficialName()

setGeneOfficialName

public void setGeneOfficialName(String geneOfficialName)

getGeneOfficialSymbol

public String getGeneOfficialSymbol()

setGeneOfficialSymbol

public void setGeneOfficialSymbol(String geneOfficialSymbol)

getIsNegativeEvidence

public boolean getIsNegativeEvidence()

setIsNegativeEvidence

public void setIsNegativeEvidence(boolean isNegativeEvidence)

getLastUpdated

public Long getLastUpdated()

setLastUpdated

public void setLastUpdated(Long lastUpdated)

getPhenotypes

public Set<CharacteristicValueObject> getPhenotypes()

setPhenotypes

public void setPhenotypes(Set<CharacteristicValueObject> phenotypes)

getPhenotypesValueUri

public Set<String> getPhenotypesValueUri()

getScoreValueObject

public ScoreValueObject getScoreValueObject()

setScoreValueObject

public void setScoreValueObject(ScoreValueObject scoreValueObject)

getTaxonCommonName

public String getTaxonCommonName()

setTaxonCommonName

public void setTaxonCommonName(String taxonCommonName)

getRelationship

public String getRelationship()

setRelationship

public void setRelationship(String relationship)

isContainQueryPhenotype

public boolean isContainQueryPhenotype()

setContainQueryPhenotype

public void setContainQueryPhenotype(boolean containQueryPhenotype)

isHomologueEvidence

public boolean isHomologueEvidence()

setHomologueEvidence

public void setHomologueEvidence(boolean isHomologueEvidence)

getPhenotypeAssPubVO

public Set<PhenotypeAssPubValueObject> getPhenotypeAssPubVO()

setPhenotypeAssPubVO

public void setPhenotypeAssPubVO(Set<PhenotypeAssPubValueObject> phenotypeAssPubVO)

getOriginalPhenotype

public String getOriginalPhenotype()

setOriginalPhenotype

public void setOriginalPhenotype(String originalPhenotype)

getPhenotypeMapping

public String getPhenotypeMapping()

setPhenotypeMapping

public void setPhenotypeMapping(String phenotypeMapping)

findPhenotypeMappingAsEnum

public PhenotypeMappingType findPhenotypeMappingAsEnum()