Package ubic.gemma.persistence.service.genome.taxon

Class TaxonServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<Taxon>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<Taxon,TaxonValueObject>

ubic.gemma.persistence.service.genome.taxon.TaxonServiceImpl

All Implemented Interfaces:

BaseImmutableService<Taxon>, BaseReadOnlyService<Taxon>, BaseService<Taxon>, BaseVoEnabledService<Taxon,TaxonValueObject>, FilteringService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>, TaxonService

@Service
public class TaxonServiceImpl
extends AbstractFilteringVoEnabledService<Taxon,TaxonValueObject>
implements TaxonService

Author:

keshav

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
TaxonServiceImpl(TaxonDao taxonDao)

Method Summary

Modifier and Type	Method	Description
Taxon	findByCommonName(String commonName)
Taxon	findByNcbiId(Integer ncbiId)
Taxon	findByScientificName(String scientificName)
Collection<TaxonValueObject>	getTaxaWithArrays()
Collection<TaxonValueObject>	getTaxaWithDatasets()
Collection<TaxonValueObject>	getTaxaWithGenes()
Collection<Taxon>	loadAllTaxaWithGenes()
void	setArrayDesignService(ArrayDesignService arrayDesignService)
void	setExpressionExperimentService(ExpressionExperimentService expressionExperimentService)
void	updateGenesUsable(Taxon taxon, boolean isGenesUsable)

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService

create, create

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.BaseService

save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.FilteringService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

Methods inherited from interface ubic.gemma.persistence.service.FilteringVoEnabledService

loadValueObjects, loadValueObjects

Methods inherited from interface ubic.gemma.persistence.service.genome.taxon.TaxonService

findOrCreate, remove, remove, remove

Constructor Details

TaxonServiceImpl

@Autowired
public TaxonServiceImpl(TaxonDao taxonDao)

Method Details

setExpressionExperimentService

@Autowired
public void setExpressionExperimentService(ExpressionExperimentService expressionExperimentService)

setArrayDesignService

@Autowired
public void setArrayDesignService(ArrayDesignService arrayDesignService)

findByCommonName

@Transactional(readOnly=true)
public Taxon findByCommonName(String commonName)

Specified by:

findByCommonName in interface TaxonService

See Also:

• TaxonService.findByCommonName(String)

findByScientificName

@Transactional(readOnly=true)
public Taxon findByScientificName(String scientificName)

Specified by:

findByScientificName in interface TaxonService

See Also:

• TaxonService.findByScientificName(String)

findByNcbiId

@Transactional(readOnly=true)
public Taxon findByNcbiId(Integer ncbiId)

Specified by:

findByNcbiId in interface TaxonService

loadAllTaxaWithGenes

@Transactional(readOnly=true)
public Collection<Taxon> loadAllTaxaWithGenes()

Specified by:

loadAllTaxaWithGenes in interface TaxonService

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithGenes

@Transactional(readOnly=true)
public Collection<TaxonValueObject> getTaxaWithGenes()

Specified by:

getTaxaWithGenes in interface TaxonService

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithDatasets

@Transactional(readOnly=true)
public Collection<TaxonValueObject> getTaxaWithDatasets()

Specified by:

getTaxaWithDatasets in interface TaxonService

Returns:

collection of taxa that have expression experiments available.

getTaxaWithArrays

@Transactional(readOnly=true)
public Collection<TaxonValueObject> getTaxaWithArrays()

Specified by:

getTaxaWithArrays in interface TaxonService

Returns:

List of taxa with array designs in gemma

updateGenesUsable

@Transactional
public void updateGenesUsable(Taxon taxon,
 boolean isGenesUsable)

Specified by:

updateGenesUsable in interface TaxonService