Package ubic.gemma.persistence.service.common.description

Interface CharacteristicDao

All Superinterfaces:

BaseDao<Characteristic>, BaseVoEnabledDao<Characteristic,CharacteristicValueObject>, BrowsingDao<Characteristic>, FilteringDao<Characteristic>, FilteringVoEnabledDao<Characteristic,CharacteristicValueObject>

All Known Implementing Classes:

CharacteristicDaoImpl

public interface CharacteristicDao
extends BrowsingDao<Characteristic>, FilteringVoEnabledDao<Characteristic,CharacteristicValueObject>

See Also:

• Characteristic

Method Summary

Modifier and Type	Method	Description
List<Characteristic>	browse(int start, int limit)	Browse through the characteristics, excluding GO annotations.
List<Characteristic>	browse(int start, int limit, String sortField, boolean descending)	Browse through the characteristics, excluding GO annotations, with sorting.
Map<String,Long>	countByValueUriGroupedByNormalizedValue(Collection<String> uris, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Count characteristics matching the provided value URIs.
Characteristic	findBestByUri(String uri)	Return the characteristic with the most frequently used non-null value by URI.
Collection<Characteristic>	findByCategory(String value)
Collection<Characteristic>	findByCategoryLike(String query, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Characteristic>	findByCategoryUri(String uri, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)
Collection<Characteristic>	findByParentClasses(Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, String category, int maxResults)
Collection<Characteristic>	findByUri(String uri, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Find characteristics with the given URI.
Collection<Characteristic>	findByValue(String search)
Collection<Characteristic>	findByValueLike(String search, String category, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents, int maxResults)	Finds all Characteristics whose value match the given search term
Map<String,Characteristic>	findByValueLikeGroupedByNormalizedValue(String valueLike, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Find characteristics by value matching the provided LIKE pattern.
Map<String,Characteristic>	findByValueUriGroupedByNormalizedValue(String valueUri, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Find characteristics by URI.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentReferencesByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	Similar to findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	findExperimentsByUris(Collection<String> uris, boolean includeSubjects, boolean includePredicates, boolean includeObjects, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Collection<Class<? extends Identifiable>>	getParentClasses()	Obtain the classes of entities can can own a Characteristic.
Map<Characteristic,Identifiable>	getParents(Collection<Characteristic> characteristics, Collection<Class<? extends Identifiable>> parentClasses, boolean includeNoParents)	Obtain the parents (i.e.

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

browse

List<Characteristic> browse(int start,
 int limit)

Browse through the characteristics, excluding GO annotations.

Specified by:

browse in interface BrowsingDao<Characteristic>

Parameters:

start - How far into the list to start

limit - Maximum records to retrieve (might be subject to security filtering)

Returns:

characteristics

browse

List<Characteristic> browse(int start,
 int limit,
 String sortField,
 boolean descending)

Browse through the characteristics, excluding GO annotations, with sorting.

Specified by:

browse in interface BrowsingDao<Characteristic>

Parameters:

start - query offset

limit - maximum amount of entries

sortField - order field

descending - order direction

Returns:

characteristics

findByParentClasses

Collection<Characteristic> findByParentClasses(@Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 @Nullable
 String category,
 int maxResults)

findByCategory

Collection<Characteristic> findByCategory(String value)

findByCategoryLike

Collection<Characteristic> findByCategoryLike(String query,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

findByCategoryUri

Collection<Characteristic> findByCategoryUri(String uri,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

findExperimentsByUris

Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentsByUris(Collection<String> uris,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 @Nullable
 Taxon taxon,
 int limit,
 boolean rankByLevel)

This search looks at direct annotations, factor values and biomaterials in that order.

Resulting EEs are filtered by ACLs.

The returned collection of EEs is effectively a Set, but since we cannot use since this should be interchangable with findExperimentReferencesByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean).

Ranking results by level guarantees correctness if a limit is used as datasets matched by direct annotation will be considered before those matched by factor values or biomaterials. It is however expensive.

Parameters:

uris - collection of URIs used for matching characteristics (via Characteristic.getValueUri())

includeSubjects - lookup subjects (or values for regular characteristics)

includePredicates - lookup predicates (only applicable to Statements)

includeObjects - lookup objects (only applicable to Statements)

taxon - taxon to restrict EEs to, or null to ignore

limit - limit how many results to return. Set to -1 for no limit.

rankByLevel - rank results by level before limiting, has no effect if limit is -1

Returns:

map of classes (ExpressionExperiment, FactorValue, BioMaterial) to the matching URI to EEs which have an associated characteristic using the given URI. The class lets us track where the annotation was.

findExperimentReferencesByUris

Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>> findExperimentReferencesByUris(Collection<String> uris,
 boolean includeSubjects,
 boolean includePredicates,
 boolean includeObjects,
 @Nullable
 Taxon taxon,
 int limit,
 boolean rankByLevel)

Similar to findExperimentsByUris(Collection, boolean, boolean, boolean, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.

See Also:

• Session.load(Object, Serializable)

findByUri

Collection<Characteristic> findByUri(String uri,
 @Nullable
 String category,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

Find characteristics with the given URI.

Parameters:

category - restrict the category of the characteristic, or null to ignore

parentClasses - only return characteristics that have parents of these classes, or null to ignore

includeNoParents - include characteristics that have no parents

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

findBestByUri

Characteristic findBestByUri(String uri)

Return the characteristic with the most frequently used non-null value by URI.

findByValueUriGroupedByNormalizedValue

Map<String,Characteristic> findByValueUriGroupedByNormalizedValue(String valueUri,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents)

Find characteristics by URI.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

findByValueLikeGroupedByNormalizedValue

Map<String,Characteristic> findByValueLikeGroupedByNormalizedValue(String valueLike,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents)

Find characteristics by value matching the provided LIKE pattern.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

countByValueUriGroupedByNormalizedValue

Map<String,Long> countByValueUriGroupedByNormalizedValue(Collection<String> uris,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents)

Count characteristics matching the provided value URIs.

The mapping key is the normalized value of the characteristics as per CharacteristicUtils.getNormalizedValue(Characteristic).

findByValue

Collection<Characteristic> findByValue(String search)

findByValueLike

Collection<Characteristic> findByValueLike(String search,
 @Nullable
 String category,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents,
 int maxResults)

Finds all Characteristics whose value match the given search term

Parameters:

category - constraint the category of the characteristic, or null to ignore

getParentClasses

Collection<Class<? extends Identifiable>> getParentClasses()

Obtain the classes of entities can can own a Characteristic.

getParents

Map<Characteristic,Identifiable> getParents(Collection<Characteristic> characteristics,
 @Nullable
 Collection<Class<? extends Identifiable>> parentClasses,
 boolean includeNoParents)

Obtain the parents (i.e. owners) of the given characteristics.

Parameters:

characteristics - characteristics to find parents for

parentClasses - restrict the parents to these classes, all parents are returned if null. If supplied, at least one parent must be provided unless includeNoParents is true.

includeNoParents - include characteristics that have no parents, those will be mapped explicitly to null.

Returns:

the supplied characteristics mapped to their parents, or null if the characteristic has no parent and includeNoParents is true. A characteristic may not have multiple parents.