Uses of Class
ubic.gemma.persistence.util.Slice

Packages that use Slice

Package	Description
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.ontology
ubic.gemma.core.visualization
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util
ubic.gemma.rest.util.args

Uses of Slice in ubic.gemma.core.loader.expression.geo.service

Methods in ubic.gemma.core.loader.expression.geo.service that return Slice

Modifier and Type	Method	Description
Slice<GeoRecord>	GeoBrowser.getRecentGeoRecords(GeoRecordType recordType, int start, int pageSize)	Retrieve recent GEO records from GEO browser.
Slice<GeoRecord>	GeoBrowserImpl.getRecentGeoRecords(GeoRecordType recordType, int start, int pageSize)
default Slice<GeoRecord>	GeoBrowser.retrieveGeoRecords(GeoQuery query, int start, int pageSize)
Slice<GeoRecord>	GeoBrowser.retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config)	Retrieve records from a GEO query.
Slice<GeoRecord>	GeoBrowserImpl.retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config)
default Slice<GeoRecord>	GeoBrowser.searchAndRetrieveGeoRecords(GeoRecordType recordType, String searchTerms, GeoSearchField field, Collection<String> allowedTaxa, Collection<String> limitPlatforms, Collection<GeoSeriesType> seriesTypes, int start, int pageSize, boolean detailed)	Search and retrieve GEO records.

Uses of Slice in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology that return Slice

Modifier and Type	Method	Description
Slice<OntologyIndividual>	FactorValueOntologyService.getFactorValues(int offset, int limit)	Obtain all the factor value in the ontology.
Slice<OntologyIndividual>	FactorValueOntologyServiceImpl.getFactorValues(int offset, int limit)
Slice<String>	FactorValueOntologyService.getFactorValueUris(int offset, int limit)	Obtain all the factor value URIs in the ontology.
Slice<String>	FactorValueOntologyServiceImpl.getFactorValueUris(int offset, int limit)

Uses of Slice in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return Slice

Modifier and Type	Method	Description
Slice<CompositeSequence>	ExpressionDataHeatmap.getDesignElements()
Slice<? extends BulkExpressionDataVector>	ExpressionDataHeatmap.getVectors()

Methods in ubic.gemma.core.visualization with parameters of type Slice

Modifier and Type	Method	Description
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a given set of design elements.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromDesignElements(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a subset using design elements.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperiment ee, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a given set of vectors.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a subset.

Uses of Slice in ubic.gemma.persistence.service

Methods in ubic.gemma.persistence.service that return Slice

Modifier and Type	Method	Description
Slice<O>	AbstractCriteriaFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
Slice<O>	AbstractFilteringVoEnabledService.load(Filters filters, Sort sort, int offset, int limit)
final Slice<O>	AbstractNoopFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
Slice<O>	AbstractQueryFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
Slice<O>	FilteringDao.load(Filters filters, Sort sort, int offset, int limit)	Load a slice of entities matching the given filters.
Slice<O>	FilteringService.load(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	AbstractCriteriaFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	AbstractFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
final Slice<VO>	AbstractNoopFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	FilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)	Load VOs with ordering, filtering and offset/limit.
Slice<VO>	FilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	CachedFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<O>	AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<O>	CachedFilteringDao.loadWithCache(Filters filters, Sort sort, int offset, int limit)

Uses of Slice in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return Slice

Modifier and Type	Method	Description
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDaoImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetServiceImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)

Uses of Slice in ubic.gemma.persistence.service.common.auditAndSecurity

Methods in ubic.gemma.persistence.service.common.auditAndSecurity that return Slice

Modifier and Type	Method	Description
Slice<C>	SecurableFilteringVoEnabledService.load(Filters filters, Sort sort, int offset, int limit)
Slice<VO>	SecurableFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)

Uses of Slice in ubic.gemma.persistence.service.expression.arrayDesign

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return Slice

Modifier and Type	Method	Description
Slice<ArrayDesignValueObject>	ArrayDesignDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)	No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
Slice<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)

Uses of Slice in ubic.gemma.persistence.service.expression.bioAssayData

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return Slice

Modifier and Type	Method	Description
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorService.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)

Uses of Slice in ubic.gemma.persistence.service.expression.designElement

Methods in ubic.gemma.persistence.service.expression.designElement that return Slice

Modifier and Type	Method	Description
Slice<CompositeSequence>	CompositeSequenceDao.findByGene(Gene gene, int start, int limit)
Slice<CompositeSequence>	CompositeSequenceDaoImpl.findByGene(Gene gene, int start, int limit)
Slice<Gene>	CompositeSequenceDao.getGenes(CompositeSequence compositeSequence, int offset, int limit)	given a composite sequence returns a collection of genes
Slice<Gene>	CompositeSequenceDaoImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit)
Slice<Gene>	CompositeSequenceService.getGenes(CompositeSequence compositeSequence, int offset, int limit)
Slice<Gene>	CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit)
Slice<CompositeSequenceValueObject>	CompositeSequenceService.loadValueObjectsForGene(Gene gene, int start, int limit)
Slice<CompositeSequenceValueObject>	CompositeSequenceServiceImpl.loadValueObjectsForGene(Gene gene, int start, int limit)

Uses of Slice in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return Slice

Modifier and Type	Method	Description
Slice<FactorValue>	FactorValueDao.loadAll(int offset, int limit)	Load a slice of FactorValues.
Slice<FactorValue>	FactorValueDaoImpl.loadAll(int offset, int limit)
Slice<FactorValue>	FactorValueService.loadAll(int offset, int limit)	Load a slice of FactorValues.
Slice<FactorValue>	FactorValueServiceImpl.loadAll(int offset, int limit)
Slice<Long>	FactorValueDao.loadAllIds(int offset, int limit)	Load a slice of the factor values IDs.
Slice<Long>	FactorValueDaoImpl.loadAllIds(int offset, int limit)
Slice<Long>	FactorValueService.loadAllIds(int offset, int limit)	Load a slice of the factor values IDs.
Slice<Long>	FactorValueServiceImpl.loadAllIds(int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Special method for front-end access.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)

Uses of Slice in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return Slice

Modifier and Type	Method	Description
<S> Slice<S>	Slice.map(Function<? super O,? extends S> converter)

Uses of Slice in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type Slice

Modifier	Constructor	Description
	FilteredAndInferredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndPaginatedResponseDataObject(Slice<T> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject(Slice<DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)

Uses of Slice in ubic.gemma.rest.util

Methods in ubic.gemma.rest.util that return Slice

Modifier and Type	Method	Description
Slice<T>	Responders.FilterMethod.load(Filters filters, Sort sort, int offset, int limit)

Methods in ubic.gemma.rest.util with parameters of type Slice

Modifier and Type	Method	Description
static <T> PaginatedResponseDataObject<T>	Responders.paginate(Slice<T> payload, String[] groupBy)	Paginate results.
static <T> QueriedAndFilteredAndPaginatedResponseDataObject<T>	Responders.paginate(Slice<T> payload, String query, Filters filters, String[] groupBy)	Paginate results with a filter and a full-text query.
static <T> FilteredAndPaginatedResponseDataObject<T>	Responders.paginate(Slice<T> payload, Filters filters, String[] groupBy)	Paginate results with a filter.

Constructors in ubic.gemma.rest.util with parameters of type Slice

Modifier	Constructor	Description
	FilteredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy)
	PaginatedResponseDataObject(Slice<T> payload, String[] groupBy)
	QueriedAndFilteredAndPaginatedResponseDataObject(Slice<T> payload, String query, Filters filters, String[] groupBy)

Uses of Slice in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return Slice

Modifier and Type	Method	Description
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset)	Retrieves the Elements of the Platform that this argument represents.
Slice<ExpressionExperimentValueObject>	PlatformArgService.getExperiments(PlatformArg<?> arg, int limit, int offset)	Retrieves the Datasets of the Platform that this argument represents.
Slice<CompositeSequenceValueObject>	GeneArgService.getGeneProbes(GeneArg<?> geneArg, int offset, int limit)	Obtain probes for the gene across all platforms.
Slice<CompositeSequenceValueObject>	GeneArgService.getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit)	Obtain probes for the gene in the given taxon across all platforms.
Slice<GeneValueObject>	GeneArgService.getGenes(int offset, int limit)
Slice<GeneValueObject>	GeneArgService.getGenesInTaxon(Taxon taxon, int offset, int limit)