Package ubic.gemma.model.association.phenotype

Class PhenotypeAssociation

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.common.auditAndSecurity.AbstractAuditable

ubic.gemma.model.association.phenotype.PhenotypeAssociation

All Implemented Interfaces:

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

Direct Known Subclasses:

DataAnalysisEvidence, ExperimentalEvidence, GenericEvidence, LiteratureEvidence

@Deprecated
public abstract class PhenotypeAssociation
extends AbstractAuditable
implements Securable

Deprecated.

Represents abstract evidence for the association of a gene with a phenotype.

Author:

Paul

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
PhenotypeAssociation()	Deprecated. No-arg constructor added to satisfy javabean contract

Method Summary

Modifier and Type	Method	Description
Characteristic	getAssociationType()	Deprecated.
GOEvidenceCode	getEvidenceCode()	Deprecated.
DatabaseEntry	getEvidenceSource()	Deprecated.
Gene	getGene()	Deprecated.
Boolean	getIsNegativeEvidence()	Deprecated.
Date	getLastUpdated()	Deprecated.
PhenotypeMappingType	getMappingType()	Deprecated.
String	getOriginalPhenotype()	Deprecated.
Set<PhenotypeAssociationPublication>	getPhenotypeAssociationPublications()	Deprecated.
Set<Characteristic>	getPhenotypes()	Deprecated.
String	getRelationship()	Deprecated.
String	getScore()	Deprecated.
QuantitationType	getScoreType()	Deprecated.
Double	getStrength()	Deprecated.
void	setAssociationType(Characteristic associationType)	Deprecated.
void	setEvidenceCode(GOEvidenceCode evidenceCode)	Deprecated.
void	setEvidenceSource(DatabaseEntry evidenceSource)	Deprecated.
void	setGene(Gene gene)	Deprecated.
void	setIsNegativeEvidence(Boolean isNegativeEvidence)	Deprecated.
void	setLastUpdated(Date lastUpdated)	Deprecated.
void	setMappingType(PhenotypeMappingType mappingType)	Deprecated.
void	setOriginalPhenotype(String originalPhenotype)	Deprecated.
void	setPhenotypeAssociationPublications(Set<PhenotypeAssociationPublication> phenotypeAssociationPublications)	Deprecated.
void	setPhenotypes(Set<Characteristic> phenotypes)	Deprecated.
void	setRelationship(String relationship)	Deprecated.
void	setScore(String score)	Deprecated.
void	setScoreType(QuantitationType scoreType)	Deprecated.
void	setStrength(Double strength)	Deprecated.

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

getAuditTrail, setAuditTrail

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

equals, getDescription, getId, getName, hashCode, setDescription, setId, setName, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.model.common.Identifiable

getId

Methods inherited from interface gemma.gsec.model.Securable

getId

Constructor Detail

PhenotypeAssociation

public PhenotypeAssociation()

Deprecated.

No-arg constructor added to satisfy javabean contract

Method Detail

getAssociationType

public Characteristic getAssociationType()

Deprecated.

Returns:

Describes the nature of the link between (genetic or physiological variation in) the gene and the phenotype, such as "predisposes to" or "causes".

setAssociationType

public void setAssociationType(Characteristic associationType)

Deprecated.

getEvidenceCode

public GOEvidenceCode getEvidenceCode()

Deprecated.

setEvidenceCode

public void setEvidenceCode(GOEvidenceCode evidenceCode)

Deprecated.

getEvidenceSource

public DatabaseEntry getEvidenceSource()

Deprecated.

Returns:

An optional external identifiable source for the evidence, if it does not come from with the system. Used to flag evidence that is imported from other phenotype databases, for example.

setEvidenceSource

public void setEvidenceSource(DatabaseEntry evidenceSource)

Deprecated.

getGene

public Gene getGene()

Deprecated.

setGene

public void setGene(Gene gene)

Deprecated.

getIsNegativeEvidence

public Boolean getIsNegativeEvidence()

Deprecated.

Returns:

If true, this association is a negative one: it indicates the evidence argues against an association between the gene and the phenotype. The default value is false. Use of this field should follow curator guidelines.

setIsNegativeEvidence

public void setIsNegativeEvidence(Boolean isNegativeEvidence)

Deprecated.

getPhenotypes

public Set<Characteristic> getPhenotypes()

Deprecated.

Returns:

The phenotype this association is about. A phenotype is (basically) a term from a controlled vocabulary such as a disease.

setPhenotypes

public void setPhenotypes(Set<Characteristic> phenotypes)

Deprecated.

getScore

public String getScore()

Deprecated.

Returns:

A score, either provided by the system or (often) imported from an external source. If this is populated, the scoreType should be populated.

setScore

public void setScore(String score)

Deprecated.

getScoreType

public QuantitationType getScoreType()

Deprecated.

Returns:

Describes the score associated with the evidence.

setScoreType

public void setScoreType(QuantitationType scoreType)

Deprecated.

getStrength

public Double getStrength()

Deprecated.

Returns:

The relative strength of the evidence, where higher values are better. This strength may be based on human curation could be from an outside source), automated criteria, or a combination of the two.

setStrength

public void setStrength(Double strength)

Deprecated.

getPhenotypeAssociationPublications

public Set<PhenotypeAssociationPublication> getPhenotypeAssociationPublications()

Deprecated.

setPhenotypeAssociationPublications

public void setPhenotypeAssociationPublications(Set<PhenotypeAssociationPublication> phenotypeAssociationPublications)

Deprecated.

getMappingType

public PhenotypeMappingType getMappingType()

Deprecated.

setMappingType

public void setMappingType(PhenotypeMappingType mappingType)

Deprecated.

getOriginalPhenotype

public String getOriginalPhenotype()

Deprecated.

setOriginalPhenotype

public void setOriginalPhenotype(String originalPhenotype)

Deprecated.

getRelationship

public String getRelationship()

Deprecated.

setRelationship

public void setRelationship(String relationship)

Deprecated.

getLastUpdated

public Date getLastUpdated()

Deprecated.

setLastUpdated

public void setLastUpdated(Date lastUpdated)

Deprecated.