Uses of Class
ubic.gemma.model.expression.arrayDesign.ArrayDesign

Packages that use ArrayDesign

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.util
ubic.gemma.core.analysis.preprocess.filter	This package contains classes for filtering expression data.
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.util.mapper	Utilities for mapping Identifiable entities to external identifiers.
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.core.tasks.analysis.sequence
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.common.search
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.blacklist	Service for managing blacklisted entities.
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.maintenance	Contains classes related to database maintenance.
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.taglib.arrayDesign

Uses of ArrayDesign in ubic.gemma.apps

Methods in ubic.gemma.apps that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
protected Collection<ArrayDesign>	ArrayDesignSequenceManipulatingCli.getRelatedDesigns(ArrayDesign design)	Mergees or subsumees of the platform.

Methods in ubic.gemma.apps with parameters of type ArrayDesign

Modifier and Type	Method	Description
protected Collection<ArrayDesign>	ArrayDesignSequenceManipulatingCli.getRelatedDesigns(ArrayDesign design)	Mergees or subsumees of the platform.
protected boolean	ArrayDesignSequenceManipulatingCli.isSubsumedOrMerged(ArrayDesign arrayDesign)
protected boolean	ArrayDesignProbeMapperCli.needToRun(Date skipIfLastRunLaterThan, ArrayDesign arrayDesign, Class<? extends ArrayDesignAnalysisEvent> eventClass)	Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.
protected boolean	ArrayDesignSequenceManipulatingCli.needToRun(Date skipIfLastRunLaterThan, ArrayDesign arrayDesign, Class<? extends ArrayDesignAnalysisEvent> eventClass)
protected void	ArrayDesignBlatCli.processArrayDesign(ArrayDesign design)
protected void	ArrayDesignRepeatScanCli.processArrayDesign(ArrayDesign design)
protected void	ArrayDesignSequenceManipulatingCli.processArrayDesign(ArrayDesign arrayDesign)
protected boolean	ArrayDesignSequenceManipulatingCli.shouldRun(Date skipIfLastRunLaterThan, ArrayDesign design, Class<? extends ArrayDesignAnalysisEvent> cls)
protected Serializable	ArrayDesignSequenceManipulatingCli.toBatchObject(ArrayDesign object)

Method parameters in ubic.gemma.apps with type arguments of type ArrayDesign

Modifier and Type	Method	Description
protected void	ArrayDesignAnnotationFileCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected void	ArrayDesignAuditTrailCleanupCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignBioSequenceDetachCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected void	ArrayDesignBlatCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignMapSummaryCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected void	ArrayDesignMergeCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected void	ArrayDesignProbeCleanupCLI.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignProbeMapperCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignProbeRenamerCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)	Deprecated.
protected void	ArrayDesignRepeatScanCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignSequenceAssociationCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	ArrayDesignSequenceManipulatingCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)
protected void	ArrayDesignSubsumptionTesterCli.processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)
protected void	BioSequenceCleanupCli.processArrayDesigns(Collection<ArrayDesign> arrayDesigns)

Uses of ArrayDesign in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	EntityLocator.locateArrayDesign(String identifier)
ArrayDesign	EntityLocatorImpl.locateArrayDesign(String identifier)

Uses of ArrayDesign in ubic.gemma.core.analysis.preprocess.filter

Constructor parameters in ubic.gemma.core.analysis.preprocess.filter with type arguments of type ArrayDesign

Modifier	Constructor	Description
	ExpressionExperimentFilter(Collection<ArrayDesign> arrayDesignsUsed, FilterConfig config)

Uses of ArrayDesign in ubic.gemma.core.analysis.report

Methods in ubic.gemma.core.analysis.report that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Collection<ArrayDesign>	WhatsNew.getNewArrayDesigns()
Collection<ArrayDesign>	WhatsNew.getUpdatedArrayDesigns()

Uses of ArrayDesign in ubic.gemma.core.analysis.sequence

Methods in ubic.gemma.core.analysis.sequence with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequenceMapValueObject>	ArrayDesignMapResultService.getSummaryMapValueObjects(ArrayDesign arrayDesign)
Collection<CompositeSequenceMapValueObject>	ArrayDesignMapResultServiceImpl.getSummaryMapValueObjects(ArrayDesign arrayDesign)
Collection<CompositeSequenceMapSummary>	ArrayDesignMapResultService.summarizeMapResults(ArrayDesign arrayDesign)
Collection<CompositeSequenceMapSummary>	ArrayDesignMapResultServiceImpl.summarizeMapResults(ArrayDesign arrayDesign)

Uses of ArrayDesign in ubic.gemma.core.analysis.service

Methods in ubic.gemma.core.analysis.service with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignAnnotationService.create(ArrayDesign inputAd, Boolean useGO, boolean deleteOtherFiles)	Create (or update) all the annotation files for the given platform.
void	ArrayDesignAnnotationServiceImpl.create(ArrayDesign inputAd, Boolean useGO, boolean deleteOtherFiles)
void	ArrayDesignAnnotationService.deleteExistingFiles(ArrayDesign arrayDesign)
void	ArrayDesignAnnotationServiceImpl.deleteExistingFiles(ArrayDesign ad)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, FilterConfig filterConfig, boolean logTransform)
Map<CompositeSequence,String[]>	ArrayDesignAnnotationService.readAnnotationFile(ArrayDesign arrayDesign)	This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.
Map<CompositeSequence,String[]>	ArrayDesignAnnotationServiceImpl.readAnnotationFile(ArrayDesign arrayDesign)

Uses of ArrayDesign in ubic.gemma.core.loader.expression

Methods in ubic.gemma.core.loader.expression that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ExpressionExperimentPlatformSwitchService.switchExperimentToMergedPlatform(ExpressionExperiment expExp)	Automatically identify an appropriate merged platform

Methods in ubic.gemma.core.loader.expression with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	DataUpdater.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay,SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)
void	DataUpdaterImpl.addCountData(ExpressionExperiment ee, ArrayDesign targetArrayDesign, DoubleMatrix<String,String> countMatrix, DoubleMatrix<String,String> rpkmMatrix, Map<BioAssay,SequencingMetadata> sequencingMetadata, boolean allowMissingSamples)	RNA-seq: Replaces data.
void	DataUpdater.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdaterImpl.addData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Generic but in practice used for RNA-seq.
void	ExperimentPlatformSwitchHelperService.persist(ExpressionExperiment expExp, ArrayDesign arrayDesign)
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)
void	DataUpdater.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, ExpressionDataDoubleMatrix data)	Replace the data associated with the experiment (or add it if there is none).
void	DataUpdaterImpl.replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)	Replace the data associated with the experiment (or add it if there is none).
void	ExpressionExperimentPlatformSwitchService.switchExperimentToArrayDesign(ExpressionExperiment ee, ArrayDesign arrayDesign)	If you know the array designs are already in a merged state, you should use switchExperimentToMergedPlatform

Uses of ArrayDesign in ubic.gemma.core.loader.expression.arrayDesign

Methods in ubic.gemma.core.loader.expression.arrayDesign that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignMergeService.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)	Merge array designs based on their sequence content.
ArrayDesign	ArrayDesignMergeServiceImpl.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)
ArrayDesign	ArrayDesignParser.parseOneLine(String line)	Deprecated.
ArrayDesign	ArrayDesignMergeHelperService.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)	Finalize the assembly and persistence of the merged array design.
ArrayDesign	ArrayDesignMergeHelperServiceImpl.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)

Methods in ubic.gemma.core.loader.expression.arrayDesign that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Collection<ArrayDesign>	ArrayDesignParser.getResults()	Deprecated.

Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ArrayDesign

Modifier and Type	Method	Description
protected void	ArrayDesignParser.addResult(ArrayDesign obj)	Deprecated.
void	ArrayDesignProbeMapperService.deleteOldFiles(ArrayDesign arrayDesign)	Delete outdated annotation and associated experiment files.
void	ArrayDesignProbeMapperServiceImpl.deleteOldFiles(ArrayDesign arrayDesign)
static Collection<BioSequence>	ArrayDesignSequenceAlignmentServiceImpl.getSequences(ArrayDesign ad)
static Collection<BioSequence>	ArrayDesignSequenceAlignmentServiceImpl.getSequences(ArrayDesign ad, Taxon taxon)
ArrayDesign	ArrayDesignMergeService.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)	Merge array designs based on their sequence content.
ArrayDesign	ArrayDesignMergeServiceImpl.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)
ArrayDesign	ArrayDesignMergeHelperService.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)	Finalize the assembly and persistence of the merged array design.
ArrayDesign	ArrayDesignMergeHelperServiceImpl.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)	Use this to add sequences to an existing Affymetrix design.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign)	Do probe mapping, writing the results to the database and using default settings.
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)	Annotate an array design using a direct source file.
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign)
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign design)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, boolean sensitive)	Run blat on all sequences on the array design.
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Blat blat)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design, boolean sensitive)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign design, Blat blat)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)	Read from FASTA file when the sequence file lacks any way to link the sequences back to the probes.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, Taxon taxon, boolean force)	Intended for use with array designs that use sequences that are in genbank, but the accessions need to be assigned after the array is already in the system.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType)	The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)	The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force)	For the case where the sequences are retrieved simply by the Genbank accession.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force, FastaCmd fc)	Provided primarily for testing.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, Taxon taxon, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, String[] databaseNames, boolean force, FastaCmd fc)
Taxon	ArrayDesignSequenceAlignmentService.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)	If no taxon is supplied then infer it from array.
Taxon	ArrayDesignSequenceAlignmentServiceImpl.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)
Taxon	ArrayDesignSequenceProcessingService.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)
Taxon	ArrayDesignSequenceProcessingServiceImpl.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)	If taxon is null then it has not been provided on the command line, then deduce the taxon from the arrayDesign.

Method parameters in ubic.gemma.core.loader.expression.arrayDesign with type arguments of type ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignMergeService.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)	Merge array designs based on their sequence content.
ArrayDesign	ArrayDesignMergeServiceImpl.merge(ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, String nameOfNewDesign, String shortNameOfNewDesign, boolean add)
ArrayDesign	ArrayDesignMergeHelperService.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)	Finalize the assembly and persistence of the merged array design.
ArrayDesign	ArrayDesignMergeHelperServiceImpl.persistMerging(ArrayDesign result, ArrayDesign arrayDesign, Collection<ArrayDesign> otherArrayDesigns, boolean mergeWithExisting, Collection<CompositeSequence> newProbes)

Uses of ArrayDesign in ubic.gemma.core.loader.expression.geo

Methods in ubic.gemma.core.loader.expression.geo that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	GeoConverter.convert(GeoPlatform geoPlatform)
ArrayDesign	GeoConverterImpl.convert(GeoPlatform geoPlatform)

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

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

Modifier and Type	Method	Description
ArrayDesign	GeoService.addElements(ArrayDesign targetPlatform)	For the rare cases (Exon arrays) where we load the platform in two stages.
ArrayDesign	GeoServiceImpl.addElements(ArrayDesign targetPlatform)

Methods in ubic.gemma.core.loader.expression.geo.service with parameters of type ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	GeoService.addElements(ArrayDesign targetPlatform)	For the rare cases (Exon arrays) where we load the platform in two stages.
ArrayDesign	GeoServiceImpl.addElements(ArrayDesign targetPlatform)

Uses of ArrayDesign in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell with parameters of type ArrayDesign

Modifier and Type	Method	Description
QuantitationType	SingleCellDataLoaderService.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataLoaderConfig config)	Load single-cell data, the data type is automatically detected.
QuantitationType	SingleCellDataLoaderService.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load a specific single-cell data type.
QuantitationType	SingleCellDataLoaderServiceImpl.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataLoaderConfig config)
QuantitationType	SingleCellDataLoaderServiceImpl.load(ExpressionExperiment ee, ArrayDesign platform, SingleCellDataType dataType, SingleCellDataLoaderConfig config)

Uses of ArrayDesign in ubic.gemma.core.loader.util.mapper

Methods in ubic.gemma.core.loader.util.mapper with parameters of type ArrayDesign

Modifier and Type	Method	Description
default EntityMapper.StatefulEntityMapper<CompositeSequence>	DesignElementMapper.forCandidates(ArrayDesign platform)	Create a mapper for the design elements of a given platform.

Uses of ArrayDesign in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
default Collection<SearchResult<ArrayDesign>>	SearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)

Uses of ArrayDesign in ubic.gemma.core.search.source

Methods in ubic.gemma.core.search.source that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Collection<SearchResult<ArrayDesign>>	CompositeSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)
Collection<SearchResult<ArrayDesign>>	DatabaseSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)	A general search for array designs.
Collection<SearchResult<ArrayDesign>>	HibernateSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)

Uses of ArrayDesign in ubic.gemma.core.tasks.analysis.sequence

Methods in ubic.gemma.core.tasks.analysis.sequence that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignProbeMapTaskCommand.getArrayDesign()
ArrayDesign	ArrayDesignRepeatScanTaskCommand.getArrayDesign()

Methods in ubic.gemma.core.tasks.analysis.sequence with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignProbeMapTaskCommand.setArrayDesign(ArrayDesign arrayDesign)
void	ArrayDesignRepeatScanTaskCommand.setArrayDesign(ArrayDesign arrayDesign)

Constructors in ubic.gemma.core.tasks.analysis.sequence with parameters of type ArrayDesign

Modifier	Constructor	Description
	ArrayDesignProbeMapTaskCommand(String taskId, boolean forceAnalysis, ArrayDesign arrayDesign)
	ArrayDesignRepeatScanTaskCommand(String taskId, ArrayDesign arrayDesign)	NOTE: we can't pass in a we command as they are defined in the web module, which messes up the configuration.
	ArrayDesignRepeatScanTaskCommand(ArrayDesign ad)

Uses of ArrayDesign in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type ArrayDesign

Modifier and Type	Method	Description
static DifferentialExpressionAnalysis	RandomDifferentialExpressionAnalysisUtils.randomAnalysis(BioAssaySet experimentAnalyzed, ExperimentalDesign design, ArrayDesign platform)

Uses of ArrayDesign in ubic.gemma.model.common.search

Methods in ubic.gemma.model.common.search that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	SearchSettings.getPlatformConstraint()
ArrayDesign	SearchSettingsValueObject.getPlatformConstraint()

Methods in ubic.gemma.model.common.search with parameters of type ArrayDesign

Modifier and Type	Method	Description
static SearchSettings	SearchSettings.compositeSequenceSearch(String query, ArrayDesign arrayDesign)	Convenience method to get pre-configured settings.
SearchSettings.SearchSettingsBuilder	SearchSettings.SearchSettingsBuilder.platformConstraint(ArrayDesign platformConstraint)
void	SearchSettings.setPlatformConstraint(ArrayDesign platformConstraint)
void	SearchSettingsValueObject.setPlatformConstraint(ArrayDesign platformConstraint)
SearchSettings	SearchSettings.withPlatformConstraint(ArrayDesign platformConstraint)

Uses of ArrayDesign in ubic.gemma.model.expression.arrayDesign

Methods in ubic.gemma.model.expression.arrayDesign that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ArrayDesign.getAlternativeTo()
ArrayDesign	ArrayDesign.getMergedInto()
ArrayDesign	ArrayDesign.getSubsumingArrayDesign()
static ArrayDesign	ArrayDesign.Factory.newInstance()
static ArrayDesign	ArrayDesign.Factory.newInstance(String shortName, Taxon taxon)

Methods in ubic.gemma.model.expression.arrayDesign that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Set<ArrayDesign>	ArrayDesign.getMergees()
Set<ArrayDesign>	ArrayDesign.getSubsumedArrayDesigns()

Methods in ubic.gemma.model.expression.arrayDesign with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesign.setAlternativeTo(ArrayDesign alternativeTo)
void	ArrayDesign.setMergedInto(ArrayDesign mergedInto)
void	ArrayDesign.setSubsumingArrayDesign(ArrayDesign subsumingArrayDesign)

Method parameters in ubic.gemma.model.expression.arrayDesign with type arguments of type ArrayDesign

Modifier and Type	Method	Description
static Collection<ArrayDesignValueObject>	ArrayDesignValueObject.create(Collection<ArrayDesign> subsumees)
void	ArrayDesign.setMergees(Set<ArrayDesign> mergees)
void	ArrayDesign.setSubsumedArrayDesigns(Set<ArrayDesign> subsumedArrayDesigns)

Constructors in ubic.gemma.model.expression.arrayDesign with parameters of type ArrayDesign

Modifier	Constructor	Description
	ArrayDesignValueObject(ArrayDesign ad)	This will only work if the object is thawed (lightly).

Uses of ArrayDesign in ubic.gemma.model.expression.bioAssay

Methods in ubic.gemma.model.expression.bioAssay that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	BioAssay.getArrayDesignUsed()
ArrayDesign	BioAssay.getOriginalPlatform()

Methods in ubic.gemma.model.expression.bioAssay with parameters of type ArrayDesign

Modifier and Type	Method	Description
static BioAssay	BioAssay.Factory.newInstance(String name, ArrayDesign arrayDesignUsed, BioMaterial sampleUsed)
void	BioAssay.setArrayDesignUsed(ArrayDesign arrayDesignUsed)
void	BioAssay.setOriginalPlatform(ArrayDesign originalPlatform)

Constructor parameters in ubic.gemma.model.expression.bioAssay with type arguments of type ArrayDesign

Modifier	Constructor	Description
	BioAssayValueObject(BioAssay bioAssay, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, BioAssay sourceBioAssay, boolean basic, boolean allFactorValues)

Uses of ArrayDesign in ubic.gemma.model.expression.designElement

Methods in ubic.gemma.model.expression.designElement that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	CompositeSequence.getArrayDesign()

Methods in ubic.gemma.model.expression.designElement with parameters of type ArrayDesign

Modifier and Type	Method	Description
static CompositeSequence	CompositeSequence.Factory.newInstance(String name, ArrayDesign ad)
static CompositeSequence	CompositeSequence.Factory.newInstance(String name, ArrayDesign ad, BioSequence bioSequence)
void	CompositeSequence.setArrayDesign(ArrayDesign arrayDesign)

Uses of ArrayDesign in ubic.gemma.model.expression.experiment

Constructor parameters in ubic.gemma.model.expression.experiment with type arguments of type ArrayDesign

Modifier	Constructor	Description
	ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees, Map<ArrayDesign,ArrayDesignValueObject> arrayDesignValueObjectsById, Map<BioAssay,BioAssay> bioAssay2SourceBioAssayMap, boolean includeAssays, boolean basic, boolean allFactorValues)

Uses of ArrayDesign in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Map<String,ArrayDesign>	ArrayDesignsForExperimentCache.getArrayDesignCache()

Methods in ubic.gemma.persistence.persister with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignsForExperimentCache.add(ArrayDesign arrayDesign)
void	ArrayDesignsForExperimentCache.add(ArrayDesign arrayDesign, Map<CompositeSequence,BioSequence> sequences)
void	ArrayDesignsForExperimentCache.add(ArrayDesign arrayDesign, Set<CompositeSequence> seqs)

Uses of ArrayDesign in ubic.gemma.persistence.service.blacklist

Methods in ubic.gemma.persistence.service.blacklist with parameters of type ArrayDesign

Modifier and Type	Method	Description
BlacklistedPlatform	BlacklistedEntityService.blacklistPlatform(ArrayDesign platform, String reason)	Blacklist a given platform.
BlacklistedPlatform	BlacklistedEntityServiceImpl.blacklistPlatform(ArrayDesign platform, String reason)
Collection<ExpressionExperiment>	BlacklistedEntityDao.getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	BlacklistedEntityDaoImpl.getNonBlacklistedExpressionExperiments(ArrayDesign arrayDesign)
boolean	BlacklistedEntityDao.isBlacklisted(ArrayDesign platform)
boolean	BlacklistedEntityDaoImpl.isBlacklisted(ArrayDesign platform)
boolean	BlacklistedEntityService.isBlacklisted(ArrayDesign platform)
boolean	BlacklistedEntityServiceImpl.isBlacklisted(ArrayDesign platform)

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

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

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignDaoImpl.find(ArrayDesign entity)
ArrayDesign	ArrayDesignDao.findByShortName(String shortName)
ArrayDesign	ArrayDesignDaoImpl.findByShortName(String shortName)
ArrayDesign	ArrayDesignService.findByShortName(String shortName)
ArrayDesign	ArrayDesignServiceImpl.findByShortName(String shortName)
ArrayDesign	ArrayDesignDao.findOneByAlternateName(String name)
ArrayDesign	ArrayDesignDaoImpl.findOneByAlternateName(String name)
ArrayDesign	ArrayDesignService.findOneByAlternateName(String name)
ArrayDesign	ArrayDesignServiceImpl.findOneByAlternateName(String name)
ArrayDesign	ArrayDesignDao.findOneByName(String name)
ArrayDesign	ArrayDesignDaoImpl.findOneByName(String name)
ArrayDesign	ArrayDesignService.findOneByName(String name)
ArrayDesign	ArrayDesignServiceImpl.findOneByName(String name)
ArrayDesign	ArrayDesignService.loadAndThaw(Long id)
ArrayDesign	ArrayDesignServiceImpl.loadAndThaw(Long id)
<T extends Exception> ArrayDesign	ArrayDesignService.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load a platform by ID and thaw it with ArrayDesignService.thawLite(ArrayDesign)
<T extends Exception> ArrayDesign	ArrayDesignServiceImpl.loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
ArrayDesign	ArrayDesignService.thaw(ArrayDesign arrayDesign)	Thaw a given platform.
ArrayDesign	ArrayDesignServiceImpl.thaw(ArrayDesign arrayDesign)
ArrayDesign	ArrayDesignService.thawCompositeSequences(ArrayDesign arrayDesign)	Thaw the composite sequences of a given platform
ArrayDesign	ArrayDesignServiceImpl.thawCompositeSequences(ArrayDesign arrayDesign)
ArrayDesign	ArrayDesignService.thawLite(ArrayDesign arrayDesign)	Perform a less intensive thaw of an array design: not the composite sequences.
ArrayDesign	ArrayDesignServiceImpl.thawLite(ArrayDesign arrayDesign)

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Collection<ArrayDesign>	ArrayDesignDao.findByAlternateName(String queryString)
Collection<ArrayDesign>	ArrayDesignDaoImpl.findByAlternateName(String queryString)
Collection<ArrayDesign>	ArrayDesignService.findByAlternateName(String queryString)
Collection<ArrayDesign>	ArrayDesignServiceImpl.findByAlternateName(String queryString)
Collection<ArrayDesign>	ArrayDesignDao.findByManufacturer(String queryString)
Collection<ArrayDesign>	ArrayDesignDaoImpl.findByManufacturer(String queryString)
Collection<ArrayDesign>	ArrayDesignService.findByManufacturer(String searchString)
Collection<ArrayDesign>	ArrayDesignServiceImpl.findByManufacturer(String searchString)
Collection<ArrayDesign>	ArrayDesignDao.findByName(String name)
Collection<ArrayDesign>	ArrayDesignDaoImpl.findByName(String name)
Collection<ArrayDesign>	ArrayDesignService.findByName(String name)
Collection<ArrayDesign>	ArrayDesignServiceImpl.findByName(String name)
Collection<ArrayDesign>	ArrayDesignDao.findByTaxon(Taxon taxon)
Collection<ArrayDesign>	ArrayDesignDaoImpl.findByTaxon(Taxon taxon)
Collection<ArrayDesign>	ArrayDesignService.findByTaxon(Taxon taxon)	Find by the primary taxon.
Collection<ArrayDesign>	ArrayDesignServiceImpl.findByTaxon(Taxon taxon)
Collection<ArrayDesign>	ArrayDesignDao.loadAllGenericGenePlatforms()
Collection<ArrayDesign>	ArrayDesignDaoImpl.loadAllGenericGenePlatforms()
Collection<ArrayDesign>	ArrayDesignService.loadAllGenericGenePlatforms()	Load *generic* gene-based platforms.
Collection<ArrayDesign>	ArrayDesignServiceImpl.loadAllGenericGenePlatforms()
Collection<ArrayDesign>	ArrayDesignService.thaw(Collection<ArrayDesign> aas)	Thaw a collection of platforms.
Collection<ArrayDesign>	ArrayDesignServiceImpl.thaw(Collection<ArrayDesign> aas)
Collection<ArrayDesign>	ArrayDesignService.thawCompositeSequences(Collection<ArrayDesign> ads)
Collection<ArrayDesign>	ArrayDesignServiceImpl.thawCompositeSequences(Collection<ArrayDesign> ads)
Collection<ArrayDesign>	ArrayDesignService.thawLite(Collection<ArrayDesign> arrayDesigns)
Collection<ArrayDesign>	ArrayDesignServiceImpl.thawLite(Collection<ArrayDesign> arrayDesigns)

Methods in ubic.gemma.persistence.service.expression.arrayDesign with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignDao.addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
void	ArrayDesignDaoImpl.addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
void	ArrayDesignService.addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
void	ArrayDesignServiceImpl.addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
void	ArrayDesignDao.deleteAlignmentData(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.deleteAlignmentData(ArrayDesign arrayDesign)
void	ArrayDesignService.deleteAlignmentData(ArrayDesign arrayDesign)	remove sequence alignment results associated with the bioSequences for this array design.
void	ArrayDesignServiceImpl.deleteAlignmentData(ArrayDesign arrayDesign)
void	ArrayDesignDao.deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	ArrayDesignService.deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	ArrayDesignServiceImpl.deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	ArrayDesignDao.deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	ArrayDesignService.deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	ArrayDesignServiceImpl.deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	ArrayDesignDao.deleteGeneProductAssociations(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.deleteGeneProductAssociations(ArrayDesign arrayDesign)
void	ArrayDesignService.deleteGeneProductAssociations(ArrayDesign arrayDesign)	deletes the gene product associations on the specified array design.
void	ArrayDesignServiceImpl.deleteGeneProductAssociations(ArrayDesign arrayDesign)
protected ArrayDesignValueObject	ArrayDesignDaoImpl.doLoadValueObject(ArrayDesign ad)	Loads a single value objects for the given array design.
ArrayDesign	ArrayDesignDaoImpl.find(ArrayDesign entity)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignService.getAlignments(ArrayDesign arrayDesign)	Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignServiceImpl.getAlignments(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignDao.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignDaoImpl.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignService.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>	ArrayDesignServiceImpl.getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	ArrayDesignDao.getBioSequences(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	ArrayDesignDaoImpl.getBioSequences(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	ArrayDesignService.getBioSequences(ArrayDesign arrayDesign)	Return all the (unique) biosequences associated with the array design.
Map<CompositeSequence,BioSequence>	ArrayDesignServiceImpl.getBioSequences(ArrayDesign arrayDesign)
Long	ArrayDesignService.getCompositeSequenceCount(ArrayDesign arrayDesign)
Long	ArrayDesignServiceImpl.getCompositeSequenceCount(ArrayDesign arrayDesign)
Collection<CompositeSequence>	ArrayDesignService.getCompositeSequences(ArrayDesign arrayDesign)
Collection<CompositeSequence>	ArrayDesignService.getCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
Collection<CompositeSequence>	ArrayDesignServiceImpl.getCompositeSequences(ArrayDesign arrayDesign)
Collection<CompositeSequence>	ArrayDesignServiceImpl.getCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
Collection<ExpressionExperiment>	ArrayDesignDao.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignDaoImpl.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignService.getExpressionExperiments(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignServiceImpl.getExpressionExperiments(ArrayDesign arrayDesign)
long	ArrayDesignDao.getExpressionExperimentsCount(ArrayDesign arrayDesign)	Obtain the number of associated expression experiments.
long	ArrayDesignDaoImpl.getExpressionExperimentsCount(ArrayDesign arrayDesign)
long	ArrayDesignService.getExpressionExperimentsCount(ArrayDesign arrayDesign)
long	ArrayDesignServiceImpl.getExpressionExperimentsCount(ArrayDesign arrayDesign)
Collection<Gene>	ArrayDesignDao.getGenes(ArrayDesign arrayDesign)	Obtain all the genes associated to the platform.
Collection<Gene>	ArrayDesignDaoImpl.getGenes(ArrayDesign arrayDesign)
Collection<Gene>	ArrayDesignService.getGenes(ArrayDesign arrayDesign)
Collection<Gene>	ArrayDesignServiceImpl.getGenes(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignDao.getGenesByCompositeSequence(ArrayDesign arrayDesign)	Obtain all the genes associated to the platform organized by corresponding design elements.
Map<CompositeSequence,Set<Gene>>	ArrayDesignDaoImpl.getGenesByCompositeSequence(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignService.getGenesByCompositeSequence(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignServiceImpl.getGenesByCompositeSequence(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	ArrayDesignService.getSwitchedExperiments(ArrayDesign id)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
Collection<ExpressionExperiment>	ArrayDesignServiceImpl.getSwitchedExperiments(ArrayDesign arrayDesign)
long	ArrayDesignService.getSwitchedExpressionExperimentCount(ArrayDesign id)
long	ArrayDesignServiceImpl.getSwitchedExpressionExperimentCount(ArrayDesign id)
Collection<ExpressionExperiment>	ArrayDesignDao.getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.
Collection<ExpressionExperiment>	ArrayDesignDaoImpl.getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
Long	ArrayDesignDao.getSwitchedExpressionExperimentsCount(ArrayDesign arrayDesign)	Count the number of switched ExpressionExperiment from a given platform.
Long	ArrayDesignDaoImpl.getSwitchedExpressionExperimentsCount(ArrayDesign arrayDesign)
Collection<Taxon>	ArrayDesignDao.getTaxa(ArrayDesign arrayDesign)
Collection<Taxon>	ArrayDesignDaoImpl.getTaxa(ArrayDesign arrayDesign)
Collection<Taxon>	ArrayDesignService.getTaxa(ArrayDesign arrayDesign)	Return the taxa for the array design.
Collection<Taxon>	ArrayDesignServiceImpl.getTaxa(ArrayDesign arrayDesign)
protected void	ArrayDesignDaoImpl.initializeCachedFilteringResult(ArrayDesign ad)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignDao.loadAlignments(ArrayDesign arrayDesign)
Map<CompositeSequence,Collection<BlatResult>>	ArrayDesignDaoImpl.loadAlignments(ArrayDesign arrayDesign)
Collection<CompositeSequence>	ArrayDesignDao.loadCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
Collection<CompositeSequence>	ArrayDesignDaoImpl.loadCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
long	ArrayDesignDao.numBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignService.numBioSequences(ArrayDesign arrayDesign)	returns the number of bioSequences associated with this ArrayDesign id
long	ArrayDesignServiceImpl.numBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignDao.numBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignService.numBlatResults(ArrayDesign arrayDesign)	returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.
long	ArrayDesignServiceImpl.numBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignDao.numCompositeSequences(ArrayDesign id)
long	ArrayDesignDaoImpl.numCompositeSequences(ArrayDesign arrayDesign)
long	ArrayDesignDao.numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignService.numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignServiceImpl.numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	ArrayDesignDao.numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignService.numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignServiceImpl.numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	ArrayDesignDao.numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	ArrayDesignService.numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	ArrayDesignServiceImpl.numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	ArrayDesignDao.numExperiments(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numExperiments(ArrayDesign arrayDesign)
long	ArrayDesignService.numExperiments(ArrayDesign arrayDesign)
long	ArrayDesignServiceImpl.numExperiments(ArrayDesign arrayDesign)
long	ArrayDesignDao.numGenes(ArrayDesign arrayDesign)
long	ArrayDesignDaoImpl.numGenes(ArrayDesign arrayDesign)
long	ArrayDesignService.numGenes(ArrayDesign arrayDesign)	Returns the number of unique Genes associated with this ArrayDesign id
long	ArrayDesignServiceImpl.numGenes(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.remove(ArrayDesign arrayDesign)
void	ArrayDesignDao.removeBiologicalCharacteristics(ArrayDesign arrayDesign)
void	ArrayDesignDaoImpl.removeBiologicalCharacteristics(ArrayDesign arrayDesign)
void	ArrayDesignService.removeBiologicalCharacteristics(ArrayDesign arrayDesign)	Remove all associations that this array design has with BioSequences.
void	ArrayDesignServiceImpl.removeBiologicalCharacteristics(ArrayDesign arrayDesign)
void	ArrayDesignDao.thaw(ArrayDesign arrayDesign)	Thaw the given platform as per ArrayDesignDao.thawLite(ArrayDesign) with its probes and genes.
void	ArrayDesignDaoImpl.thaw(ArrayDesign arrayDesign)
ArrayDesign	ArrayDesignService.thaw(ArrayDesign arrayDesign)	Thaw a given platform.
ArrayDesign	ArrayDesignServiceImpl.thaw(ArrayDesign arrayDesign)
void	ArrayDesignDao.thawCompositeSequences(ArrayDesign arrayDesign)	Only thaw the design elements of a given platform.
void	ArrayDesignDaoImpl.thawCompositeSequences(ArrayDesign arrayDesign)
ArrayDesign	ArrayDesignService.thawCompositeSequences(ArrayDesign arrayDesign)	Thaw the composite sequences of a given platform
ArrayDesign	ArrayDesignServiceImpl.thawCompositeSequences(ArrayDesign arrayDesign)
void	ArrayDesignDao.thawLite(ArrayDesign arrayDesign)	Lightly thaw the given platform.
void	ArrayDesignDaoImpl.thawLite(ArrayDesign arrayDesign)
ArrayDesign	ArrayDesignService.thawLite(ArrayDesign arrayDesign)	Perform a less intensive thaw of an array design: not the composite sequences.
ArrayDesign	ArrayDesignServiceImpl.thawLite(ArrayDesign arrayDesign)
boolean	ArrayDesignDao.updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)
boolean	ArrayDesignDaoImpl.updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)
boolean	ArrayDesignService.updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)	Test whether the candidateSubsumer subsumes the candidateSubsumee.
boolean	ArrayDesignServiceImpl.updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)

Method parameters in ubic.gemma.persistence.service.expression.arrayDesign with type arguments of type ArrayDesign

Modifier and Type	Method	Description
Map<CompositeSequence,Set<Gene>>	ArrayDesignDao.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignDaoImpl.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignService.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignServiceImpl.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Collection<ArrayDesign>	ArrayDesignService.thaw(Collection<ArrayDesign> aas)	Thaw a collection of platforms.
Collection<ArrayDesign>	ArrayDesignServiceImpl.thaw(Collection<ArrayDesign> aas)
Collection<ArrayDesign>	ArrayDesignService.thawCompositeSequences(Collection<ArrayDesign> ads)
Collection<ArrayDesign>	ArrayDesignServiceImpl.thawCompositeSequences(Collection<ArrayDesign> ads)
Collection<ArrayDesign>	ArrayDesignService.thawLite(Collection<ArrayDesign> arrayDesigns)
Collection<ArrayDesign>	ArrayDesignServiceImpl.thawLite(Collection<ArrayDesign> arrayDesigns)

Uses of ArrayDesign in ubic.gemma.persistence.service.expression.bioAssay

Method parameters in ubic.gemma.persistence.service.expression.bioAssay with type arguments of type ArrayDesign

Modifier and Type	Method	Description
List<BioAssayValueObject>	BioAssayDao.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign,ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)

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

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	RawExpressionDataVectorDao.find(ArrayDesign arrayDesign, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDaoImpl.find(ArrayDesign arrayDesign, QuantitationType quantitationType)

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

Methods in ubic.gemma.persistence.service.expression.designElement with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequence>	CompositeSequenceDao.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceService.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByGene(Gene gene, ArrayDesign arrayDesign)
CompositeSequence	CompositeSequenceDao.findByName(ArrayDesign arrayDesign, String name)
CompositeSequence	CompositeSequenceDaoImpl.findByName(ArrayDesign arrayDesign, String name)
CompositeSequence	CompositeSequenceService.findByName(ArrayDesign arrayDesign, String name)
CompositeSequence	CompositeSequenceServiceImpl.findByName(ArrayDesign arrayDesign, String name)
Collection<Object[]>	CompositeSequenceDao.getRawSummary(ArrayDesign arrayDesign, int numResults)
Collection<Object[]>	CompositeSequenceDaoImpl.getRawSummary(ArrayDesign arrayDesign, int numResults)
Collection<Object[]>	CompositeSequenceService.getRawSummary(ArrayDesign arrayDesign, int numResults)
Collection<Object[]>	CompositeSequenceServiceImpl.getRawSummary(ArrayDesign arrayDesign, int numResults)

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

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
Map<ArrayDesign,Long>	ExpressionExperimentDao.getArrayDesignsUsageFrequency(int maxResults)	Obtain dataset usage frequency by platform currently used.
Map<ArrayDesign,Long>	ExpressionExperimentDao.getArrayDesignsUsageFrequency(Collection<Long> eeIds, int maxResults)	Obtain dataset usage frequency by platform currently for the given dataset IDs.
Map<ArrayDesign,Long>	ExpressionExperimentDaoImpl.getArrayDesignsUsageFrequency(int maxResults)
Map<ArrayDesign,Long>	ExpressionExperimentDaoImpl.getArrayDesignsUsageFrequency(Collection<Long> eeIds, int maxResults)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(Collection<ExpressionExperiment> ees)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment bas)
Collection<ArrayDesign>	ExpressionExperimentDao.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(Collection<ExpressionExperiment> ees)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment bas)
Collection<ArrayDesign>	ExpressionExperimentDaoImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	ExpressionExperimentService.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt)
Collection<ArrayDesign>	ExpressionExperimentServiceImpl.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)
Collection<ArrayDesign>	ExpressionExperimentSubSetDao.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetDaoImpl.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetService.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetServiceImpl.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Map<ArrayDesign,Long>	ExpressionExperimentService.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)	Calculate the usage frequency of platforms by the datasets matching the provided filters.
Map<ArrayDesign,Long>	ExpressionExperimentServiceImpl.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
Map<ArrayDesign,Long>	ExpressionExperimentDao.getOriginalPlatformsUsageFrequency(int maxResults)	Obtain dataset usage frequency by original platforms.
Map<ArrayDesign,Long>	ExpressionExperimentDao.getOriginalPlatformsUsageFrequency(Collection<Long> eeIds, int maxResults)	Obtain dataset usage frequency by platform currently for the given dataset IDs.
Map<ArrayDesign,Long>	ExpressionExperimentDaoImpl.getOriginalPlatformsUsageFrequency(int maxResults)
Map<ArrayDesign,Long>	ExpressionExperimentDaoImpl.getOriginalPlatformsUsageFrequency(Collection<Long> eeIds, int maxResults)

Uses of ArrayDesign in ubic.gemma.persistence.service.genome

Methods in ubic.gemma.persistence.service.genome with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequence>	GeneDao.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)	Get the composite sequences (e.g.
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)

Uses of ArrayDesign in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequence>	GeneService.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)
Collection<CompositeSequence>	GeneServiceImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)

Uses of ArrayDesign in ubic.gemma.persistence.service.maintenance

Methods in ubic.gemma.persistence.service.maintenance with parameters of type ArrayDesign

Modifier and Type	Method	Description
int	TableMaintenanceUtil.updateGene2CsEntries(ArrayDesign arrayDesign, boolean force)	Update the GENE2CS table for a specific ArrayDesign.
int	TableMaintenanceUtilImpl.updateGene2CsEntries(ArrayDesign arrayDesign, boolean force)

Uses of ArrayDesign in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return types with arguments of type ArrayDesign

Modifier and Type	Method	Description
static Collection<ArrayDesign>	CommonQueries.getArrayDesignsUsed(Collection<? extends BioAssaySet> ees, Session session)	Retrieve a list of array designs used by the given experiments.
static Collection<ArrayDesign>	CommonQueries.getArrayDesignsUsed(BioAssaySet bas, Session session)	Retrieve a list of array designs used in given expression experiment

Methods in ubic.gemma.persistence.util with parameters of type ArrayDesign

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, ArrayDesign arrayDesign)
static void	BusinessKey.checkValidKey(ArrayDesign arrayDesign)
static Criteria	BusinessKey.createQueryObject(Session session, ArrayDesign arrayDesign)
EntityUrlBuilder.ArrayDesignUrl	EntityUrlBuilder.EntityUrlChooser.entity(ArrayDesign entity)

Constructors in ubic.gemma.persistence.util with parameters of type ArrayDesign

Modifier	Constructor	Description
	ArrayDesignUrl(String baseUrl, ArrayDesign entity)
	ArrayDesignWebUrl(String baseUrl, ArrayDesign entity)

Uses of ArrayDesign in ubic.gemma.rest

Method parameters in ubic.gemma.rest with type arguments of type ArrayDesign

Modifier and Type	Method	Description
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getBlacklistedPlatforms(FilterArg<ArrayDesign> filter, SortArg<ArrayDesign> sort, OffsetArg offset, LimitArg limit)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getBlacklistedPlatforms(FilterArg<ArrayDesign> filter, SortArg<ArrayDesign> sort, OffsetArg offset, LimitArg limit)
ResponseDataObject<Long>	PlatformsWebService.getNumberOfPlatforms(FilterArg<ArrayDesign> filter)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatforms(FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatforms(FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatformsByIds(PlatformArrayArg platformsArg, FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)	Retrieves all datasets matching the given identifiers.
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatformsByIds(PlatformArrayArg platformsArg, FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)	Retrieves all datasets matching the given identifiers.

Constructor parameters in ubic.gemma.rest with type arguments of type ArrayDesign

Modifier	Constructor	Description
	ExpressionExperimentSubsetWithFactorValuesObject(ExpressionExperimentSubSet subset, Set<FactorValue> factorValues, Map<ArrayDesign,ArrayDesignValueObject> id2advo, boolean includeAssays, Map<BioAssay,BioAssay> assay2sourceAssayMap)

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

Methods in ubic.gemma.rest.util.args with parameters of type ArrayDesign

Modifier and Type	Method	Description
CompositeSequence	CompositeSequenceArgService.getEntityWithPlatform(CompositeSequenceArg<?> probeArg, ArrayDesign platform)
void	CompositeSequenceArrayArg.setPlatform(ArrayDesign arrayDesign)

Uses of ArrayDesign in ubic.gemma.web.controller.expression.arrayDesign

Methods in ubic.gemma.web.controller.expression.arrayDesign that return ArrayDesign

Modifier and Type	Method	Description
ArrayDesign	ArrayDesignAddCommand.getArrayDesign()

Methods in ubic.gemma.web.controller.expression.arrayDesign with parameters of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequenceMapValueObject>	ArrayDesignController.getDesignSummaries(ArrayDesign arrayDesign)
void	ArrayDesignAddCommand.setArrayDesign(ArrayDesign arrayDesign)

Method parameters in ubic.gemma.web.controller.expression.arrayDesign with type arguments of type ArrayDesign

Modifier and Type	Method	Description
Collection<CompositeSequenceMapValueObject>	ArrayDesignController.getCsSummaries(EntityDelegator<ArrayDesign> ed)
Map<String,String>	ArrayDesignController.getReportHtml(EntityDelegator<ArrayDesign> ed)
String	ArrayDesignController.remove(EntityDelegator<ArrayDesign> ed)
String	ArrayDesignController.updateReport(EntityDelegator<ArrayDesign> ed)

Uses of ArrayDesign in ubic.gemma.web.taglib.arrayDesign

Methods in ubic.gemma.web.taglib.arrayDesign with parameters of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignGroupingTag.setSubsumer(ArrayDesign subsumer)

Method parameters in ubic.gemma.web.taglib.arrayDesign with type arguments of type ArrayDesign

Modifier and Type	Method	Description
void	ArrayDesignGroupingTag.setSubsumees(Collection<ArrayDesign> subsumees)