Package ubic.gemma.model.genome.sequenceAnalysis

Class AnnotationAssociation

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 final class	AnnotationAssociation.Factory

Constructor Summary

Constructors

Constructor	Description
AnnotationAssociation()

Method Summary

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 Details

AnnotationAssociation

public AnnotationAssociation()

Method Details

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