AnnotationAssociation (Gemma 1.32.0 API)

java.lang.Object
- ubic.gemma.model.common.AbstractIdentifiable
- - ubic.gemma.model.association.BioSequence2GeneProduct
  - - ubic.gemma.model.genome.sequenceAnalysis.AnnotationAssociation

All Implemented Interfaces:

Identifiable
```
public class AnnotationAssociation
extends BioSequence2GeneProduct
```
An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis. Importantly, the 'overlap', 'score' and other parameters will not be filled in. Also note that in these cases the associated BioSequence may not have actual sequence information filled in. This type of association is used as a "last resort" annotation source for the following types of situations: No sequence information is available; annotations are unavailable (e.g., non-model organisms); or sequences are too short to align using our usual methods (e.g., miRNAs).

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class AnnotationAssociation.Factory

Constructor Summary

Constructors
Constructor Description

AnnotationAssociation()

Method Summary

All Methods Instance Methods Concrete Methods
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.
`ExternalDatabase`	`getSource()`
`int`	`hashCode()`	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
`void`	`setSource(ExternalDatabase source)`

Methods inherited from class ubic.gemma.model.association.BioSequence2GeneProduct
getBioSequence, getGeneProduct, getOverlap, getScore, getSourceAnalysis, getSpecificity, getThreePrimeDistance, getThreePrimeDistanceMeasurementMethod, setBioSequence, setGeneProduct, setOverlap, setScore, setSourceAnalysis, setSpecificity, setThreePrimeDistance, setThreePrimeDistanceMeasurementMethod

Methods inherited from class ubic.gemma.model.common.AbstractIdentifiable
getId, setId, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - AnnotationAssociation
```
public AnnotationAssociation()
```
- Method Detail
  - getSource
```
public ExternalDatabase getSource()
```
    Returns:
    
    The original source of the annotation, such as GEO or flyBase.
  - setSource
```
public void setSource(ExternalDatabase source)
```
  - 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.
    
    Specified by:
    
    hashCode in class AbstractIdentifiable
  - 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