Package ubic.gemma.model.analysis.sequence

Class GeneMappingSummary

java.lang.Object

ubic.gemma.model.analysis.sequence.GeneMappingSummary

All Implemented Interfaces:

Serializable

public class GeneMappingSummary
extends Object
implements Serializable

This is a convenience value object to hold a BlatResult and its associated gene products and genes.

Author:

jsantos, paul

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
GeneMappingSummary()

Method Summary

Modifier and Type	Method	Description
void	addGene(GeneProductValueObject geneProduct, GeneValueObject gene)
BlatResultValueObject	getBlatResult()
String	getBlatResultId()
CompositeSequenceValueObject	getCompositeSequence()
GeneValueObject	getGene(GeneProductValueObject geneProduct)
Map<String,GeneValueObject>	getGeneProductIdGeneMap()
Map<String,GeneProductValueObject>	getGeneProductIdMap()
Map<GeneProductValueObject,GeneValueObject>	getGeneProductMap()
Collection<GeneProductValueObject>	getGeneProducts()
double	getIdentity()
double	getScore()
void	setBlatResult(BlatResultValueObject blatResult2)
void	setCompositeSequence(CompositeSequenceValueObject compositeSequence)
void	setGeneProductMap(Map<GeneProductValueObject,GeneValueObject> geneProductMap)

Methods inherited from class java.lang.Object

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

Constructor Details

GeneMappingSummary

public GeneMappingSummary()

Method Details

getBlatResult

public BlatResultValueObject getBlatResult()

Returns:

the blatResult

setBlatResult

public void setBlatResult(BlatResultValueObject blatResult2)

Parameters:

blatResult2 - the blatResult to set

getGeneProductMap

public Map<GeneProductValueObject,GeneValueObject> getGeneProductMap()

Returns:

the geneProductMap

setGeneProductMap

public void setGeneProductMap(Map<GeneProductValueObject,GeneValueObject> geneProductMap)

Parameters:

geneProductMap - the geneProductMap to set

getGeneProducts

public Collection<GeneProductValueObject> getGeneProducts()

getGene

public GeneValueObject getGene(GeneProductValueObject geneProduct)

addGene

public void addGene(GeneProductValueObject geneProduct,
 GeneValueObject gene)

getGeneProductIdGeneMap

public Map<String,GeneValueObject> getGeneProductIdGeneMap()

getGeneProductIdMap

public Map<String,GeneProductValueObject> getGeneProductIdMap()

getIdentity

public double getIdentity()

getScore

public double getScore()

getBlatResultId

public String getBlatResultId()

getCompositeSequence

public CompositeSequenceValueObject getCompositeSequence()

setCompositeSequence

public void setCompositeSequence(CompositeSequenceValueObject compositeSequence)