Package ubic.gemma.persistence.service.genome.gene

Class GeneSetValueObjectHelperImpl

java.lang.Object

ubic.gemma.persistence.service.genome.gene.GeneSetValueObjectHelperImpl

All Implemented Interfaces:

GeneSetValueObjectHelper

@Component
public class GeneSetValueObjectHelperImpl
extends Object
implements GeneSetValueObjectHelper

This class will handle population of GeneSetValueObjects. Services need to be accessed in order to define values for size, geneIds, and public/private fields.

Author:

tvrossum

Constructor Summary

Constructors

Constructor	Description
GeneSetValueObjectHelperImpl()

Method Summary

Modifier and Type	Method	Description
GOGroupValueObject	convertToGOValueObject(GeneSet gs, String goId, String searchTerm)	Method to create a GO group object from an ad hoc entity
DatabaseBackedGeneSetValueObject	convertToLightValueObject(GeneSet gs)	Constructor to build value object from GeneSet.
List<DatabaseBackedGeneSetValueObject>	convertToLightValueObjects(Collection<GeneSet> geneSets, boolean includeOnesWithoutGenes)	results will be sorted by size
DatabaseBackedGeneSetValueObject	convertToValueObject(GeneSet gs)	Constructor to build value object from GeneSet.
List<DatabaseBackedGeneSetValueObject>	convertToValueObjects(Collection<GeneSet> sets)
List<DatabaseBackedGeneSetValueObject>	convertToValueObjects(Collection<GeneSet> genesets, boolean includeOnesWithoutGenes)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneSetValueObjectHelperImpl

public GeneSetValueObjectHelperImpl()

Method Detail

convertToGOValueObject

public GOGroupValueObject convertToGOValueObject(GeneSet gs,
                                                 String goId,
                                                 String searchTerm)

Description copied from interface: GeneSetValueObjectHelper

Method to create a GO group object from an ad hoc entity

Specified by:

convertToGOValueObject in interface GeneSetValueObjectHelper

Parameters:

gs - gene set

goId - gene ontology id

searchTerm - search term

Returns:

Go group VO

convertToLightValueObject

public DatabaseBackedGeneSetValueObject convertToLightValueObject(GeneSet gs)

Description copied from interface: GeneSetValueObjectHelper

Constructor to build value object from GeneSet. This is a light version and *does not include member ids*! (But the size is set.) No security filtering is done here, assuming that if the user could load the experimentSet entity, they have access to it.

Specified by:

convertToLightValueObject in interface GeneSetValueObjectHelper

Parameters:

gs - the expressionExperimentSet entity to create a value object for

Returns:

a gene set value object with all fields filled except for gene members

convertToLightValueObjects

public List<DatabaseBackedGeneSetValueObject> convertToLightValueObjects(Collection<GeneSet> geneSets,
                                                                         boolean includeOnesWithoutGenes)

Description copied from interface: GeneSetValueObjectHelper

results will be sorted by size

Specified by:

convertToLightValueObjects in interface GeneSetValueObjectHelper

Parameters:

geneSets - gene sets

includeOnesWithoutGenes - if true, even gene sets that lack genes will be returned.

Returns:

list of gene set value objects

convertToValueObject

public DatabaseBackedGeneSetValueObject convertToValueObject(GeneSet gs)

Description copied from interface: GeneSetValueObjectHelper

Constructor to build value object from GeneSet. No security filtering is done here, assuming that if the user could load the experimentSet entity, they have access to it.

Specified by:

convertToValueObject in interface GeneSetValueObjectHelper

Parameters:

gs - an expressionExperimentSet entity to create a value object for

Returns:

a new DatabaseBackedGeneSetValueObject

convertToValueObjects

public List<DatabaseBackedGeneSetValueObject> convertToValueObjects(Collection<GeneSet> sets)

Specified by:

convertToValueObjects in interface GeneSetValueObjectHelper

Parameters:

sets - gene sets

Returns:

results will be sorted by size gene sets that lack genes will be excluded

convertToValueObjects

public List<DatabaseBackedGeneSetValueObject> convertToValueObjects(Collection<GeneSet> genesets,
                                                                    boolean includeOnesWithoutGenes)

Specified by:

convertToValueObjects in interface GeneSetValueObjectHelper

Parameters:

genesets - gene sets

includeOnesWithoutGenes - if true, even gene sets that lack genes will be returned.

Returns:

results will be sorted by size