Package ubic.gemma.core.genome.gene

Interface GeneSetValueObjectHelper

All Known Implementing Classes:

GeneSetValueObjectHelperImpl

public interface GeneSetValueObjectHelper

* @author tvrossum

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)

Method Detail

convertToGOValueObject

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

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

Parameters:

goId - gene ontology id

gs - gene set

searchTerm - search term

Returns:

Go group VO

convertToLightValueObject

DatabaseBackedGeneSetValueObject convertToLightValueObject(GeneSet gs)

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.

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

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

results will be sorted by size

Parameters:

genesets - gene sets

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

Returns:

list of gene set value objects

convertToValueObject

DatabaseBackedGeneSetValueObject convertToValueObject(GeneSet gs)

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.

Parameters:

gs - an expressionExperimentSet entity to create a value object for

Returns:

a new DatabaseBackedGeneSetValueObject

convertToValueObjects

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

Parameters:

sets - gene sets

Returns:

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

convertToValueObjects

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

Parameters:

geneSets - gene sets

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

Returns:

results will be sorted by size