Package ubic.gemma.model.association

Class BioSequence2GeneProduct

java.lang.Object

ubic.gemma.model.association.BioSequence2GeneProduct

All Implemented Interfaces:

Serializable, Identifiable

Direct Known Subclasses:

AnnotationAssociation, BlatAssociation, ReferenceAssociation

public abstract class BioSequence2GeneProduct
extends Object
implements Identifiable, Serializable

An association between a BioSequence and a Gene Product. This class is abstract and is variously subclassed with BlatAssociation in order to capture the scores and other parameters that document why we think there is a connection between a given sequence and a gene product.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
BioSequence2GeneProduct()

Method Summary

Modifier and Type	Method	Description
BioSequence	getBioSequence()
GeneProduct	getGeneProduct()
Long	getId()
Integer	getOverlap()
Double	getScore()
Analysis	getSourceAnalysis()
Double	getSpecificity()
Long	getThreePrimeDistance()
ThreePrimeDistanceMethod	getThreePrimeDistanceMeasurementMethod()
void	setBioSequence(BioSequence bioSequence)
void	setGeneProduct(GeneProduct geneProduct)
void	setId(Long id)
void	setOverlap(Integer overlap)
void	setScore(Double score)
void	setSourceAnalysis(Analysis sourceAnalysis)
void	setSpecificity(Double specificity)
void	setThreePrimeDistance(Long threePrimeDistance)
void	setThreePrimeDistanceMeasurementMethod(ThreePrimeDistanceMethod threePrimeDistanceMeasurementMethod)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioSequence2GeneProduct

public BioSequence2GeneProduct()

Method Detail

getBioSequence

public BioSequence getBioSequence()

setBioSequence

public void setBioSequence(BioSequence bioSequence)

getGeneProduct

public GeneProduct getGeneProduct()

Returns:

A collection of GeneProducts that this BioSequence2GeneProduct corresponds to. A BioSequence can align to one or more GeneProducts.

setGeneProduct

public void setGeneProduct(GeneProduct geneProduct)

getId

public Long getId()

Specified by:

getId in interface Identifiable

setId

public void setId(Long id)

getOverlap

public Integer getOverlap()

Returns:

Degree to which the sequence overlaps with the gene product. This is often the overlap of a DNA sequence with the exons encoding the mRNA for the GeneProduct, but could have other interpretations

setOverlap

public void setOverlap(Integer overlap)

getScore

public Double getScore()

Returns:

The score for the association between the biosequence and the gene product. This could be a BLAT similarity or other score.

setScore

public void setScore(Double score)

getSourceAnalysis

public Analysis getSourceAnalysis()

setSourceAnalysis

public void setSourceAnalysis(Analysis sourceAnalysis)

getSpecificity

public Double getSpecificity()

Returns:

A measure of how specific this association is compared to others that were obtained in the same analysis. This can be misleading if the same sequence was analyzed multiple times with different algorithms, databases, or parameters. High values are "better" but the exactly interpretation is implementation-specific.

setSpecificity

public void setSpecificity(Double specificity)

getThreePrimeDistance

public Long getThreePrimeDistance()

Returns:

The distance from the 3' end where this BioSequence aligns with respect to the Gene Product. This is often the location of the alignment with respect to an mRNA 3' end.

setThreePrimeDistance

public void setThreePrimeDistance(Long threePrimeDistance)

getThreePrimeDistanceMeasurementMethod

public ThreePrimeDistanceMethod getThreePrimeDistanceMeasurementMethod()

Returns:

Specifies the method used to measure the distance from the threePrimeEnd.

setThreePrimeDistanceMeasurementMethod

public void setThreePrimeDistanceMeasurementMethod(ThreePrimeDistanceMethod threePrimeDistanceMeasurementMethod)