Package ubic.gemma.persistence.service.expression.experiment

Interface FactorValueDao

All Superinterfaces:

BaseDao<FactorValue>, BaseVoEnabledDao<FactorValue,FactorValueValueObject>, FilteringDao<FactorValue>, FilteringVoEnabledDao<FactorValue,FactorValueValueObject>

All Known Implementing Classes:

FactorValueDaoImpl

public interface FactorValueDao
extends FilteringVoEnabledDao<FactorValue,FactorValueValueObject>

See Also:

• FactorValue

Method Summary

Modifier and Type	Method	Description
Collection<FactorValue>	findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated.
Map<FactorValue,Characteristic>	getExperimentalFactorCategories(Collection<FactorValue> factorValues)
Map<FactorValue,ExpressionExperiment>	getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)
Slice<FactorValue>	loadAll(int offset, int limit)	Load a slice of FactorValues.
Collection<Long>	loadAllIds()	Load all factor value IDs.
Slice<Long>	loadAllIds(int offset, int limit)	Load a slice of the factor values IDs.
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)	Deprecated.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
void	updateIgnoreAcl(FactorValue fv)	Deprecated. do not use this, it is only a workaround to make FV migration faster

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

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

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

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

loadValueObjects, loadValueObjects

Method Details

loadAll

Slice<FactorValue> loadAll(int offset,
 int limit)

Load a slice of FactorValues.

Results are filtered by ACL on the owning ExpressionExperiment.

loadAllIds

Collection<Long> loadAllIds()

Load all factor value IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

loadAllIds

Slice<Long> loadAllIds(int offset,
 int limit)

Load a slice of the factor values IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

findByValueStartingWith

@Deprecated
Collection<FactorValue> findByValueStartingWith(String valuePrefix,
 int maxResults)

Deprecated.

Locate based on string value of the value.

Results are filtered by ACL on the owning ExpressionExperiment.

Parameters:

valuePrefix - value prefix

maxResults - maximum number of results to return, or -1 for no limit

Returns:

collection of factor values

loadWithOldStyleCharacteristics

@Deprecated
FactorValue loadWithOldStyleCharacteristics(Long id,
 boolean readOnly)

Deprecated.

loadIdsWithNumberOfOldStyleCharacteristics

@Deprecated
Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)

Deprecated.

Load all the factor values IDs with their number of old-style characteristics.

Parameters:

excludedIds - list of excluded IDs

getExperimentalFactorCategories

Map<FactorValue,Characteristic> getExperimentalFactorCategories(Collection<FactorValue> factorValues)

getExpressionExperimentsIgnoreAcls

Map<FactorValue,ExpressionExperiment> getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)

updateIgnoreAcl

@Deprecated
void updateIgnoreAcl(FactorValue fv)

Deprecated.

do not use this, it is only a workaround to make FV migration faster

Update a FactorValue without involving ACL advice.