java.lang.Object
- ubic.gemma.model.common.AbstractDescribable
- - ubic.gemma.model.common.AbstractAuditable
  - - ubic.gemma.model.association.phenotype.PhenotypeAssociation

All Implemented Interfaces:

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

Direct Known Subclasses:

DataAnalysisEvidence, ExperimentalEvidence, GenericEvidence, LiteratureEvidence
```
@Deprecated
public abstract class PhenotypeAssociation
extends AbstractAuditable
implements gemma.gsec.model.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

All Methods Instance Methods Concrete Methods Deprecated Methods
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.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.

Class PhenotypeAssociation

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface gemma.gsec.model.Securable

Constructor Detail

PhenotypeAssociation

Method Detail

getAssociationType

setAssociationType

getEvidenceCode

setEvidenceCode

getEvidenceSource

setEvidenceSource

getGene

setGene

getIsNegativeEvidence

setIsNegativeEvidence

getPhenotypes

setPhenotypes

getScore

setScore

getScoreType

setScoreType

getStrength

setStrength

getPhenotypeAssociationPublications

setPhenotypeAssociationPublications

getMappingType

setMappingType

getOriginalPhenotype

setOriginalPhenotype

getRelationship

setRelationship

getLastUpdated

setLastUpdated