Class ExpressionExperimentSetDaoImpl
- java.lang.Object
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- ubic.gemma.persistence.service.AbstractDao<O>
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- ubic.gemma.persistence.service.AbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
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- ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl
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- All Implemented Interfaces:
ExpressionExperimentSetDao
,BaseDao<ExpressionExperimentSet>
,BaseVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
@Repository public class ExpressionExperimentSetDaoImpl extends AbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject> implements ExpressionExperimentSetDao
- Author:
- paul
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Field Summary
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Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
REPORT_SLOW_QUERY_AFTER_MS
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Fields inherited from class ubic.gemma.persistence.service.AbstractDao
elementClass, log
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Constructor Summary
Constructors Constructor Description ExpressionExperimentSetDaoImpl(SessionFactory sessionFactory, ExpressionExperimentDao expressionExperimentDao)
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Method Summary
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Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects
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Methods inherited from class ubic.gemma.persistence.service.AbstractDao
countAll, create, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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Constructor Detail
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ExpressionExperimentSetDaoImpl
@Autowired public ExpressionExperimentSetDaoImpl(SessionFactory sessionFactory, ExpressionExperimentDao expressionExperimentDao)
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Method Detail
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find
public Collection<ExpressionExperimentSet> find(BioAssaySet bioAssaySet)
- Specified by:
find
in interfaceExpressionExperimentSetDao
- Parameters:
bioAssaySet
- bio assay set- Returns:
- expressionExperimentSets that contain the given bioAssaySet.
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findByName
public Collection<ExpressionExperimentSet> findByName(String name)
- Specified by:
findByName
in interfaceExpressionExperimentSetDao
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getExperimentsInSet
public Collection<ExpressionExperiment> getExperimentsInSet(Long id)
- Specified by:
getExperimentsInSet
in interfaceExpressionExperimentSetDao
- Parameters:
id
- id- Returns:
- the security-filtered list of experiments in a set. It is possible for the return to be empty even if the set is not (due to security filters). Use this instead of expressionExperimentSet.getExperiments.
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loadAllExperimentSetsWithTaxon
public Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()
- Specified by:
loadAllExperimentSetsWithTaxon
in interfaceExpressionExperimentSetDao
- Returns:
- ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.
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thaw
public void thaw(ExpressionExperimentSet expressionExperimentSet)
- Specified by:
thaw
in interfaceExpressionExperimentSetDao
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loadAllValueObjects
public Collection<ExpressionExperimentSetValueObject> loadAllValueObjects(boolean loadEEIds)
- Specified by:
loadAllValueObjects
in interfaceExpressionExperimentSetDao
- Parameters:
loadEEIds
- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- ee vos
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loadValueObjects
public List<ExpressionExperimentSetValueObject> loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)
- Specified by:
loadValueObjects
in interfaceExpressionExperimentSetDao
- Parameters:
eeSetIds
- idsloadEEIds
- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- ee vos
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getExperimentValueObjectsInSet
public Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)
- Specified by:
getExperimentValueObjectsInSet
in interfaceExpressionExperimentSetDao
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loadValueObject
public ExpressionExperimentSetValueObject loadValueObject(Long id, boolean loadEEIds)
- Specified by:
loadValueObject
in interfaceExpressionExperimentSetDao
- Parameters:
id
- idloadEEIds
- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- ee vos
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doLoadValueObject
protected ExpressionExperimentSetValueObject doLoadValueObject(ExpressionExperimentSet entity)
Description copied from class:AbstractVoEnabledDao
Load a value object for a given entity.This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement
AbstractVoEnabledDao.postProcessValueObjects(List)
instead.- Specified by:
doLoadValueObject
in classAbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
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doLoadValueObjects
public List<ExpressionExperimentSetValueObject> doLoadValueObjects(Collection<ExpressionExperimentSet> entities)
Description copied from class:AbstractVoEnabledDao
Load all the value objects for the given entities.The default is to apply
AbstractVoEnabledDao.doLoadValueObject(Identifiable)
on each entry and weed out null elements.This method should be fast and any post-processing should happen in
AbstractVoEnabledDao.postProcessValueObjects(List)
.- Overrides:
doLoadValueObjects
in classAbstractVoEnabledDao<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
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