Uses of Class
ubic.gemma.model.genome.TaxonValueObject

Packages that use TaxonValueObject

Package	Description
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.taxon
ubic.gemma.rest
ubic.gemma.web.controller.genome.gene

Uses of TaxonValueObject in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff that return types with arguments of type TaxonValueObject

Modifier and Type	Method	Description
Set<TaxonValueObject>	DifferentialExpressionAnalysisResultSetValueObject.getTaxa()

Method parameters in ubic.gemma.model.analysis.expression.diff with type arguments of type TaxonValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResultSetValueObject.setTaxa(Set<TaxonValueObject> taxa)

Uses of TaxonValueObject in ubic.gemma.model.expression.arrayDesign

Methods in ubic.gemma.model.expression.arrayDesign that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	ArrayDesignValueObject.getTaxonObject()

Methods in ubic.gemma.model.expression.arrayDesign with parameters of type TaxonValueObject

Modifier and Type	Method	Description
void	ArrayDesignValueObject.setTaxonObject(TaxonValueObject taxonObject)

Uses of TaxonValueObject in ubic.gemma.model.expression.experiment

Methods in ubic.gemma.model.expression.experiment that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	ExpressionExperimentValueObject.getTaxonObject()	FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().

Methods in ubic.gemma.model.expression.experiment with parameters of type TaxonValueObject

Modifier and Type	Method	Description
void	ExpressionExperimentValueObject.setTaxonObject(TaxonValueObject taxonObject)	FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().

Uses of TaxonValueObject in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return TaxonValueObject

Modifier and Type	Method	Description
static TaxonValueObject	TaxonValueObject.fromEntity(Taxon taxon)
TaxonValueObject	PhysicalLocationValueObject.getTaxon()

Methods in ubic.gemma.model.genome with parameters of type TaxonValueObject

Modifier and Type	Method	Description
void	PhysicalLocationValueObject.setTaxon(TaxonValueObject taxon)

Uses of TaxonValueObject in ubic.gemma.model.genome.gene

Methods in ubic.gemma.model.genome.gene that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	GeneSetValueObject.getTaxon()
TaxonValueObject	GeneValueObject.getTaxon()
TaxonValueObject	GeneValueObject.getTaxonForGemmaRest()

Methods in ubic.gemma.model.genome.gene with parameters of type TaxonValueObject

Modifier and Type	Method	Description
void	GeneSetValueObject.setTaxon(TaxonValueObject taxon)
void	GeneValueObject.setTaxon(TaxonValueObject taxon)

Uses of TaxonValueObject in ubic.gemma.model.genome.sequenceAnalysis

Methods in ubic.gemma.model.genome.sequenceAnalysis that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	BioSequenceValueObject.getTaxon()
TaxonValueObject	BlatResultValueObject.getTaxon()

Methods in ubic.gemma.model.genome.sequenceAnalysis with parameters of type TaxonValueObject

Modifier and Type	Method	Description
void	BioSequenceValueObject.setTaxon(TaxonValueObject taxon)
void	BlatResultValueObject.setTaxon(TaxonValueObject taxon)

Constructors in ubic.gemma.model.genome.sequenceAnalysis with parameters of type TaxonValueObject

Modifier	Constructor	Description
	BlatResultValueObject(Long id, TaxonValueObject taxon, Integer blockCount, String blockSizes, Integer matches, Integer mismatches, Integer ns, Integer queryEnd, Integer queryGapBases, Integer queryGapCount, BioSequenceValueObject querySequence, Integer queryStart, String queryStarts, Integer repMatches, Double score, Double identity, String strand, String targetChromosomeName, String targetDatabase, Long targetEnd, Integer targetGapBases, Integer targetGapCount, Long targetStart, String targetStarts)

Uses of TaxonValueObject in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	GeneSetService.getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject geneSetVO)	get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
TaxonValueObject	GeneSetServiceImpl.getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject geneSetVO)

Uses of TaxonValueObject in ubic.gemma.persistence.service.genome.taxon

Methods in ubic.gemma.persistence.service.genome.taxon that return TaxonValueObject

Modifier and Type	Method	Description
protected TaxonValueObject	TaxonDaoImpl.doLoadValueObject(Taxon entity)

Methods in ubic.gemma.persistence.service.genome.taxon that return types with arguments of type TaxonValueObject

Modifier and Type	Method	Description
Collection<TaxonValueObject>	TaxonService.getTaxaWithArrays()
Collection<TaxonValueObject>	TaxonServiceImpl.getTaxaWithArrays()
Collection<TaxonValueObject>	TaxonService.getTaxaWithDatasets()
Collection<TaxonValueObject>	TaxonServiceImpl.getTaxaWithDatasets()
Collection<TaxonValueObject>	TaxonService.getTaxaWithGenes()
Collection<TaxonValueObject>	TaxonServiceImpl.getTaxaWithGenes()

Uses of TaxonValueObject in ubic.gemma.rest

Subclasses of TaxonValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static final class	DatasetsWebService.TaxonWithUsageStatisticsValueObject

Methods in ubic.gemma.rest that return TaxonValueObject

Modifier and Type	Method	Description
TaxonValueObject	SearchWebService.SearchSettingsValueObject.getTaxon()

Methods in ubic.gemma.rest that return types with arguments of type TaxonValueObject

Modifier and Type	Method	Description
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxa()	Lists all available taxa.
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxaByIds(TaxonArrayArg taxaArg)	Retrieves single taxon based on the given identifier.

Uses of TaxonValueObject in ubic.gemma.web.controller.genome.gene

Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type TaxonValueObject

Modifier and Type	Method	Description
Collection<TaxonValueObject>	GenePickerController.getTaxa()	AJAX
Collection<TaxonValueObject>	GenePickerController.getTaxaWithArrays()	AJAX
Collection<TaxonValueObject>	GenePickerController.getTaxaWithDatasets()	AJAX
Collection<TaxonValueObject>	GenePickerController.getTaxaWithGenes()	AJAX