Uses of Class
ubic.gemma.persistence.util.Slice
Packages that use Slice
Package
Description
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Uses of Slice in ubic.gemma.core.loader.expression.geo.service
Methods in ubic.gemma.core.loader.expression.geo.service that return SliceModifier and TypeMethodDescriptionGeoBrowser.retrieveGeoRecords(GeoQuery query, int start, int pageSize) GeoBrowser.retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config) Retrieve records from a GEO query.GeoBrowserImpl.retrieveGeoRecords(GeoQuery query, int start, int pageSize, GeoRetrieveConfig config) 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 SliceModifier and TypeMethodDescriptionFactorValueOntologyService.getFactorValues(int offset, int limit) Obtain all the factor value in the ontology.FactorValueOntologyServiceImpl.getFactorValues(int offset, int limit) FactorValueOntologyService.getFactorValueUris(int offset, int limit) Obtain all the factor value URIs in the ontology.FactorValueOntologyServiceImpl.getFactorValueUris(int offset, int limit) -
Uses of Slice in ubic.gemma.core.visualization
Methods in ubic.gemma.core.visualization that return SliceModifier and TypeMethodDescriptionExpressionDataHeatmap.getDesignElements()Slice<? extends BulkExpressionDataVector> ExpressionDataHeatmap.getVectors()Methods in ubic.gemma.core.visualization with parameters of type SliceModifier and TypeMethodDescriptionstatic ExpressionDataHeatmapExpressionDataHeatmap.fromDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes) Create a heatmap for a given set of design elements.static ExpressionDataHeatmapExpressionDataHeatmap.fromDesignElements(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes) Create a heatmap for a subset using design elements.static ExpressionDataHeatmapExpressionDataHeatmap.fromVectors(ExpressionExperiment ee, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes) Create a heatmap for a given set of vectors.static ExpressionDataHeatmapExpressionDataHeatmap.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 SliceModifier and TypeMethodDescriptionLoad a slice of entities matching the given filters.AbstractCriteriaFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit) AbstractFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit) AbstractNoopFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit) AbstractQueryFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit) FilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit) Load VOs with ordering, filtering and offset/limit.FilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit) AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) CachedFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters filters, Sort sort, int offset, int limit) 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 SliceModifier and TypeMethodDescriptionExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort) Retrieve result sets associated to a set ofBioAssaySetand external database entries.ExpressionAnalysisResultSetDaoImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort) ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort) 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 -
Uses of Slice in ubic.gemma.persistence.service.expression.arrayDesign
Methods in ubic.gemma.persistence.service.expression.arrayDesign that return SliceModifier and TypeMethodDescriptionArrayDesignDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ArrayDesignDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ArrayDesignReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ArrayDesignReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) 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.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 SliceModifier and TypeMethodDescriptionProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit) ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit) ProcessedExpressionDataVectorService.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit) 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 SliceModifier and TypeMethodDescriptionCompositeSequenceDao.findByGene(Gene gene, int start, int limit, boolean useGene2Cs) Find a slice of composite sequences mapped to a given gene.CompositeSequenceDaoImpl.findByGene(Gene gene, int start, int limit, boolean useGene2Cs) CompositeSequenceDao.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) given a composite sequence returns a collection of genesCompositeSequenceDaoImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) CompositeSequenceReadService.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) CompositeSequenceReadServiceImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) CompositeSequenceService.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs) CompositeSequenceService.loadValueObjectsForGene(Gene gene, int start, int limit, boolean useGene2Cs) CompositeSequenceServiceImpl.loadValueObjectsForGene(Gene gene, int start, int limit, boolean useGene2Cs) -
Uses of Slice in ubic.gemma.persistence.service.expression.experiment
Methods in ubic.gemma.persistence.service.expression.experiment that return SliceModifier and TypeMethodDescriptionFactorValueDao.loadAll(int offset, int limit) Load a slice ofFactorValues.FactorValueDaoImpl.loadAll(int offset, int limit) FactorValueReadService.loadAll(int offset, int limit) FactorValueReadServiceImpl.loadAll(int offset, int limit) FactorValueService.loadAll(int offset, int limit) Load a slice ofFactorValues.FactorValueServiceImpl.loadAll(int offset, int limit) FactorValueDao.loadAllIds(int offset, int limit) Load a slice of the factor values IDs.FactorValueDaoImpl.loadAllIds(int offset, int limit) FactorValueReadService.loadAllIds(int offset, int limit) FactorValueReadServiceImpl.loadAllIds(int offset, int limit) FactorValueService.loadAllIds(int offset, int limit) Load a slice of the factor values IDs.FactorValueServiceImpl.loadAllIds(int offset, int limit) ExpressionExperimentDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentDao.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) Special method for front-end access.ExpressionExperimentDaoImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentReadService.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentReadServiceImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentService.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentServiceImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentDao.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) Flavour ofExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentReadService.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentReadServiceImpl.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentService.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentServiceImpl.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentReadService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentReadServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) ExpressionExperimentServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) WorkflowService.queue(WorkflowState state, String datasetType, String assignee, Date since, int offset, int limit) Return datasets currently instate, oldest entry first (so the curator's "what's been waiting longest" view is the natural read).WorkflowServiceImpl.queue(WorkflowState state, String datasetType, String assignee, Date since, int offset, int limit) -
Uses of Slice in ubic.gemma.persistence.util
Methods in ubic.gemma.persistence.util that return Slice -
Uses of Slice in ubic.gemma.rest
Constructors in ubic.gemma.rest with parameters of type SliceModifierConstructorDescriptionFilteredAndInferredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms) FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms) PaginatedResponseDataObjectCompositeSequenceSummaryValueObject(Slice<GeneWebService.CompositeSequenceSummaryValueObject> payload, String[] groupBy) 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) QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject(Slice<ExperimentExpressionLevelsValueObject> 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 SliceModifier and TypeMethodDescriptionMethods in ubic.gemma.rest.util with parameters of type SliceModifier and TypeMethodDescriptionstatic <T> PaginatedResponseDataObject<T> Paginate results.static <T> QueriedAndFilteredAndPaginatedResponseDataObject<T> Paginate results with a filter and a full-text query.static <T> FilteredAndPaginatedResponseDataObject<T> Paginate results with a filter.Constructors in ubic.gemma.rest.util with parameters of type SliceModifierConstructorDescriptionFilteredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy) FilteredAndPaginatedResponseDataObjectArrayDesignValueObject(Slice<ArrayDesignValueObject> payload, Filters filters, String[] groupBy) FilteredAndPaginatedResponseDataObjectCompositeSequenceValueObject(Slice<CompositeSequenceValueObject> payload, Filters filters, String[] groupBy) FilteredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject(Slice<DifferentialExpressionAnalysisResultSetValueObject> payload, Filters filters, String[] groupBy) FilteredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy) FilteredAndPaginatedResponseDataObjectGeneValueObject(Slice<GeneValueObject> payload, Filters filters, String[] groupBy) PaginatedResponseDataObject(Slice<T> payload, String[] groupBy) PaginatedResponseDataObjectCompositeSequenceValueObject(Slice<CompositeSequenceValueObject> payload, String[] groupBy) PaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, String[] groupBy) PaginatedResponseDataObjectGeneValueObject(Slice<GeneValueObject> payload, String[] groupBy) PaginatedResponseDataObjectTicketValueObject(Slice<TicketValueObject> 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 SliceModifier and TypeMethodDescriptionPlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset) Retrieves the design elements of the platform that this argument represents.PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset, boolean withSequence) Variant that opt-in hydrates the probe-sequence projection (sequence + length) via a single batch HQL after the main page is fetched.PlatformArgService.getElements(PlatformArg<?> arg, int limit, int offset, boolean withSequence, boolean withGenes, Collection<Long> geneIds) Full-projection variant: adds the opt-in gene column (withGenes) and the opt-in gene restriction (geneIds).PlatformArgService.getElements(PlatformArg<?> arg, Filters userFilters, Collection<Long> geneIds, int limit, int offset, boolean withSequence, boolean withGenes) Widest offset-mode variant: user-suppliedfilter=conjunct on top of everything else.PlatformArgService.getElements(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, int limit, int offset, boolean withSequence) PlatformArgService.getElements(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg, int limit, int offset, boolean withSequence, boolean withGenes) Probe-set variant with the opt-in gene column.PlatformArgService.getExperiments(PlatformArg<?> arg, int limit, int offset) Retrieves the Datasets of the Platform that this argument represents.GeneArgService.getGeneProbes(GeneArg<?> geneArg, int offset, int limit) Obtain probes for the gene across all platforms.GeneArgService.getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit) Obtain probes for the gene in the given taxon across all platforms.GeneArgService.getGenes(int offset, int limit) GeneArgService.getGenesInTaxon(Taxon taxon, int offset, int limit)