Uses of Class
ubic.gemma.model.expression.designElement.CompositeSequence

Packages that use CompositeSequence

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.datastructure.matrix.io	This package contains I/O utilities for reading and writing expression data matrices.
ubic.gemma.core.loader.expression.arrayDesign
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.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.designElement
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression.pca
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.service.genome
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.util
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.designElement
ubic.gemma.web.controller.expression.experiment

Uses of CompositeSequence in ubic.gemma.core.analysis.expression.coexpression.links

Methods in ubic.gemma.core.analysis.expression.coexpression.links that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	LinkAnalysis.getProbe(int index)
CompositeSequence	AbstractMatrixRowPairAnalysis.getProbeForRow(ExpressionDataMatrixRowElement rowEl)
CompositeSequence	MatrixRowPairAnalysis.getProbeForRow(ExpressionDataMatrixRowElement rowEl)

Methods in ubic.gemma.core.analysis.expression.coexpression.links that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
Map<CompositeSequence,Set<Gene>>	LinkAnalysis.getProbeToGeneMap()

Method parameters in ubic.gemma.core.analysis.expression.coexpression.links with type arguments of type CompositeSequence

Modifier and Type	Method	Description
void	AbstractMatrixRowPairAnalysis.setDuplicateMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)
void	MatrixRowPairAnalysis.setDuplicateMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)
void	LinkAnalysis.setProbeToGeneMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)	Once set, is unmodifiable.

Uses of CompositeSequence in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type CompositeSequence

Modifier and Type	Method	Description
static String	DiffExAnalyzerUtils.nameForR(CompositeSequence cs)

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type CompositeSequence

Modifier and Type	Method	Description
static DoubleMatrix<String,String>	DiffExAnalyzerUtils.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.

Uses of CompositeSequence in ubic.gemma.core.analysis.preprocess.svd

Methods in ubic.gemma.core.analysis.preprocess.svd that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
DoubleMatrix<CompositeSequence,Integer>	ExpressionDataSVD.getU()

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

Methods in ubic.gemma.core.analysis.sequence that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	CompositeSequenceMapSummary.getCompositeSequence()

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

Modifier and Type	Method	Description
static CompositeSequenceMapValueObject	CompositeSequenceMapValueObject.fromEntity(CompositeSequence cs)

Method parameters in ubic.gemma.core.analysis.sequence with type arguments of type CompositeSequence

Modifier and Type	Method	Description
Collection<CompositeSequenceMapSummary>	ArrayDesignMapResultService.summarizeMapResults(Collection<CompositeSequence> compositeSequences)	Non-HQL version of the composite sequence data summary query.
Collection<CompositeSequenceMapSummary>	ArrayDesignMapResultServiceImpl.summarizeMapResults(Collection<CompositeSequence> compositeSequences)

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

Modifier	Constructor	Description
	CompositeSequenceMapSummary(CompositeSequence compositeSequence)

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

Methods in ubic.gemma.core.analysis.service that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
LinkedHashMap<Gene,Collection<CompositeSequence>>	CompositeSequenceGeneMapperService.getGene2ProbeMapByOfficialSymbols(Collection<String> officialSymbols, Collection<ArrayDesign> arrayDesigns)
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)

Method parameters in ubic.gemma.core.analysis.service with type arguments of type CompositeSequence

Modifier and Type	Method	Description
void	DiffExAnalysisResultSetWriter.write(DifferentialExpressionAnalysis analysis, Map<CompositeSequence,String[]> geneAnnotations, DifferentialExpressionAnalysisConfig config, boolean hasSignificantBatchConfound, OutputStream stream)	Write a DifferentialExpressionAnalysis as a ZIP archive containing entries for the analysis and each result set.

Uses of CompositeSequence in ubic.gemma.core.datastructure.matrix

Fields in ubic.gemma.core.datastructure.matrix with type parameters of type CompositeSequence

Modifier and Type	Field	Description
protected Map<CompositeSequence,BioAssayDimension>	AbstractMultiAssayExpressionDataMatrix.bioAssayDimensions
protected Map<Integer,CompositeSequence>	AbstractMultiAssayExpressionDataMatrix.rowDesignElementMapByInteger
protected Map<CompositeSequence,Integer>	AbstractMultiAssayExpressionDataMatrix.rowElementMap

Methods in ubic.gemma.core.datastructure.matrix that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	ExpressionDataMatrixRowElement.getDesignElement()
CompositeSequence	AbstractBulkExpressionDataMatrix.getDesignElementForRow(int index)
CompositeSequence	AbstractMultiAssayExpressionDataMatrix.getDesignElementForRow(int index)
CompositeSequence	EmptySingleCellExpressionDataMatrix.getDesignElementForRow(int index)
CompositeSequence	ExpressionDataMatrix.getDesignElementForRow(int index)	Return a design element for a given index.
CompositeSequence	MaskedExpressionDataMatrix.getDesignElementForRow(int index)
CompositeSequence	SingleCellExpressionDataDoubleMatrix.getDesignElementForRow(int index)
CompositeSequence	SingleCellExpressionDataIntMatrix.getDesignElementForRow(int index)

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
List<CompositeSequence>	AbstractBulkExpressionDataMatrix.getDesignElements()
List<CompositeSequence>	AbstractMultiAssayExpressionDataMatrix.getDesignElements()
List<CompositeSequence>	EmptySingleCellExpressionDataMatrix.getDesignElements()
List<CompositeSequence>	ExpressionDataMatrix.getDesignElements()	Obtain all the design elements in this data matrix.
List<CompositeSequence>	MaskedExpressionDataMatrix.getDesignElements()
List<CompositeSequence>	SingleCellExpressionDataDoubleMatrix.getDesignElements()
List<CompositeSequence>	SingleCellExpressionDataIntMatrix.getDesignElements()
DoubleMatrix<CompositeSequence,BioMaterial>	ExpressionDataDoubleMatrix.getMatrix()
Map<CompositeSequence,Double>	ExpressionDataDoubleMatrix.getRanks()
Map<CompositeSequence,Double>	TwoChannelExpressionDataMatrixBuilder.getRanksByMean()
List<CompositeSequence>	ExpressionDataDoubleMatrix.getRowNames()

Methods in ubic.gemma.core.datastructure.matrix with parameters of type CompositeSequence

Modifier and Type	Method	Description
protected void	AbstractMultiAssayExpressionDataMatrix.addToRowMaps(int row, CompositeSequence designElement)	Each row is a unique DesignElement.
int	AbstractMultiAssayExpressionDataMatrix.columns(CompositeSequence el)
int	MultiAssayBulkExpressionDataMatrix.columns(CompositeSequence el)	Number of columns that use the given design element.
T	AbstractBulkExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
T	AbstractMultiAssayExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
T	BulkExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
Integer	ExpressionDataIntegerMatrix.get(CompositeSequence designElement, BioMaterial bioMaterial)
BioAssayDimension	AbstractMultiAssayExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)
BioAssayDimension	MultiAssayBulkExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.
T[]	AbstractBulkExpressionDataMatrix.getRow(CompositeSequence designElement)
T[]	AbstractMultiAssayExpressionDataMatrix.getRow(CompositeSequence designElement)
Object[]	EmptySingleCellExpressionDataMatrix.getRow(CompositeSequence designElement)
T[]	ExpressionDataMatrix.getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
T[]	MaskedExpressionDataMatrix.getRow(CompositeSequence designElement)
Double[]	SingleCellExpressionDataDoubleMatrix.getRow(CompositeSequence designElement)
Integer[]	SingleCellExpressionDataIntMatrix.getRow(CompositeSequence designElement)
double[]	BulkExpressionDataDoubleMatrix.getRowAsDoubles(CompositeSequence designElement)
double[]	ExpressionDataDoubleMatrix.getRowAsDoubles(CompositeSequence designElement)
double[]	ExpressionDataPrimitiveDoubleMatrix.getRowAsDoubles(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
double[]	SingleCellExpressionDataDoubleMatrix.getRowAsDoubles(CompositeSequence designElement)
int[]	BulkExpressionDataIntMatrix.getRowAsInts(CompositeSequence designElement)
int[]	ExpressionDataPrimitiveIntMatrix.getRowAsInts(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
int[]	SingleCellExpressionDataIntMatrix.getRowAsInts(CompositeSequence designElement)
int	AbstractBulkExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	AbstractMultiAssayExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	EmptySingleCellExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	ExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	MaskedExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	SingleCellExpressionDataDoubleMatrix.getRowIndex(CompositeSequence designElement)
int	SingleCellExpressionDataIntMatrix.getRowIndex(CompositeSequence designElement)
int[]	AbstractBulkExpressionDataMatrix.getRowIndices(CompositeSequence designElement)
int[]	AbstractMultiAssayExpressionDataMatrix.getRowIndices(CompositeSequence designElement)
int[]	EmptySingleCellExpressionDataMatrix.getRowIndices(CompositeSequence designElement)
int[]	ExpressionDataMatrix.getRowIndices(CompositeSequence designElement)	Obtain all the rows that correspond to the given design element, or null if the design element is not found.
int[]	MaskedExpressionDataMatrix.getRowIndices(CompositeSequence designElement)
int[]	SingleCellExpressionDataDoubleMatrix.getRowIndices(CompositeSequence designElement)
int[]	SingleCellExpressionDataIntMatrix.getRowIndices(CompositeSequence designElement)
void	ExpressionDataDoubleMatrix.set(CompositeSequence designElement, BioAssay bioAssay, Double value)	Deprecated.

Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type CompositeSequence

Modifier and Type	Method	Description
ExpressionDataMatrix<Double>	BulkExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	BulkExpressionDataIntMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptyBulkExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptyExpressionMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Object>	EmptySingleCellExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Boolean>	ExpressionDataBooleanMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	ExpressionDataIntegerMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<T>	ExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<String>	ExpressionDataStringMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<T>	MaskedExpressionDataMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Double>	SingleCellExpressionDataDoubleMatrix.sliceRows(List<CompositeSequence> designElements)
ExpressionDataMatrix<Integer>	SingleCellExpressionDataIntMatrix.sliceRows(List<CompositeSequence> designElements)

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type CompositeSequence

Modifier	Constructor	Description
protected	AbstractBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType, List<CompositeSequence> designElements)
	ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix dmatrix, DoubleMatrix<CompositeSequence,BioMaterial> copiedMatrix)
	ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)	Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.
	ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.
	ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, Collection<CompositeSequence> designElements, QuantitationType quantitationType)

Uses of CompositeSequence in ubic.gemma.core.datastructure.matrix.io

Method parameters in ubic.gemma.core.datastructure.matrix.io with type arguments of type CompositeSequence

Modifier and Type	Method	Description
int	MatrixWriter.write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, OutputStream stream)	Write a MEX matrix as a TAR archive to the given output stream.
int	MexMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Write a matrix to a directory.
int	TabularMatrixWriter.write(Collection<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)
int	TabularMatrixWriter.write(Stream<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)
int	TabularMatrixWriter.write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)
int	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,String[]> geneAnnotations)	Alternate method that uses annotations in string form (e.g., read from another file).

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

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

Modifier and Type	Method	Description
CompositeSequence	Reporter.getCompositeSequence()
protected CompositeSequence	AffyProbeReader.getKey(Collection<Reporter> newItem)
CompositeSequence	CompositeSequenceParser.parseOneLine(String line)

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

Modifier and Type	Method	Description
Collection<CompositeSequence>	AffyProbeReader.getKeySet()
Collection<CompositeSequence>	CompositeSequenceParser.getResults()

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

Modifier and Type	Method	Description
protected void	CompositeSequenceParser.addResult(CompositeSequence obj)
boolean	AffyProbeReader.containsKey(CompositeSequence key)
Collection<Reporter>	AffyProbeReader.get(CompositeSequence key)
void	ArrayDesignProbeMapperService.printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col)	Print results to STDOUT
void	ArrayDesignProbeMapperServiceImpl.printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col)
Map<String,Collection<BlatAssociation>>	ArrayDesignProbeMapperService.processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)
Map<String,Collection<BlatAssociation>>	ArrayDesignProbeMapperServiceImpl.processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)
protected void	AffyProbeReader.put(CompositeSequence key, Collection<Reporter> value)
void	Reporter.setCompositeSequence(CompositeSequence compositeSequence)

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

Modifier and Type	Method	Description
void	ArrayDesignSequenceProcessingService.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, File fastaFile)	Associate sequences with an array design.
void	ArrayDesignSequenceProcessingService.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, InputStream fastaFile)
void	ArrayDesignSequenceProcessingService.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, Collection<BioSequence> sequences)	Associate sequences with an array design.
void	ArrayDesignSequenceProcessingServiceImpl.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, File fastaFile)
void	ArrayDesignSequenceProcessingServiceImpl.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, InputStream fastaFile)	Associate sequences with an array design.
void	ArrayDesignSequenceProcessingServiceImpl.assignSequencesToDesignElements(Collection<CompositeSequence> designElements, Collection<BioSequence> sequences)

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

Method parameters in ubic.gemma.core.loader.expression.singleCell with type arguments of type CompositeSequence

Modifier and Type	Method	Description
Stream<SingleCellExpressionDataVector>	AbstractDelegatingSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	AnnDataSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	MexSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension scd, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	NullSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	SingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.

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

Methods in ubic.gemma.core.loader.util.mapper that return types with arguments of type CompositeSequence

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

Method parameters in ubic.gemma.core.loader.util.mapper with type arguments of type CompositeSequence

Modifier and Type	Method	Description
EntityMapper.StatefulEntityMapper<CompositeSequence>	AbstractGeneIdentifierBasedDesignElementMapper.forCandidates(Collection<CompositeSequence> candidates)

Constructor parameters in ubic.gemma.core.loader.util.mapper with type arguments of type CompositeSequence

Modifier	Constructor	Description
protected	AbstractGeneIdentifierBasedDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
	EnsemblIdDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
	GeneNameDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
	MapBasedDesignElementMapper(String name, Map<String,CompositeSequence> elementsMapping)
	NcbiIdDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
	OfficialSymbolDesignElementMapper(Map<CompositeSequence,Set<Gene>> cs2g)
	SimpleDesignElementMapper(Collection<CompositeSequence> de)

Uses of CompositeSequence in ubic.gemma.core.search

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

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

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

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

Modifier and Type	Method	Description
Collection<SearchResult<CompositeSequence>>	CompositeSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	DatabaseSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	HibernateSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)

Uses of CompositeSequence in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
Slice<CompositeSequence>	ExpressionDataHeatmap.getDesignElements()

Method parameters in ubic.gemma.core.visualization with type arguments of type CompositeSequence

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.

Uses of CompositeSequence in ubic.gemma.core.visualization.cellbrowser

Method parameters in ubic.gemma.core.visualization.cellbrowser with type arguments of type CompositeSequence

Modifier and Type	Method	Description
int	CellBrowserTabularMatrixWriter.write(Collection<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)
int	CellBrowserTabularMatrixWriter.write(Stream<SingleCellExpressionDataVector> vectors, Map<CompositeSequence,Set<Gene>> cs2gene, Writer writer)

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

Methods in ubic.gemma.model.analysis.expression.diff that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	DifferentialExpressionAnalysisResult.getProbe()

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResult.setProbe(CompositeSequence probe)

Uses of CompositeSequence in ubic.gemma.model.analysis.expression.pca

Methods in ubic.gemma.model.analysis.expression.pca that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	ProbeLoading.getProbe()

Methods in ubic.gemma.model.analysis.expression.pca with parameters of type CompositeSequence

Modifier and Type	Method	Description
static ProbeLoading	ProbeLoading.Factory.newInstance(Integer componentNumber, Double loading, Integer loadingRank, CompositeSequence probe)
void	ProbeLoading.setProbe(CompositeSequence probe)

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

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

Modifier and Type	Method	Description
Set<CompositeSequence>	ArrayDesign.getCompositeSequences()

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

Modifier and Type	Method	Description
void	ArrayDesign.setCompositeSequences(Set<CompositeSequence> compositeSequences)

Uses of CompositeSequence in ubic.gemma.model.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	DesignElementDataVector.getDesignElement()

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type CompositeSequence

Modifier and Type	Method	Description
void	DesignElementDataVector.setDesignElement(CompositeSequence designElement)

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

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

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

Constructors in ubic.gemma.model.expression.designElement with parameters of type CompositeSequence

Modifier	Constructor	Description
	CompositeSequenceValueObject(CompositeSequence cs)
	CompositeSequenceValueObject(CompositeSequence cs, ArrayDesignValueObject arrayDesign)	Constructor that reuses an existing ArrayDesignValueObject.

Uses of CompositeSequence in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	ArrayDesignsForExperimentCache.getFromCache(CompositeSequence cs)

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

Modifier and Type	Method	Description
void	ArrayDesignsForExperimentCache.addToCache(CompositeSequence cs)
CompositeSequence	ArrayDesignsForExperimentCache.getFromCache(CompositeSequence cs)

Method parameters in ubic.gemma.persistence.persister with type arguments of type CompositeSequence

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

Uses of CompositeSequence in ubic.gemma.persistence.service.analysis.expression.pca

Method parameters in ubic.gemma.persistence.service.analysis.expression.pca with type arguments of type CompositeSequence

Modifier and Type	Method	Description
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence,Integer> u, double[] eigenvalues, DoubleMatrix<Integer,BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence,Integer> u, double[] eigenvalues, DoubleMatrix<Integer,BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)

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

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

Modifier and Type	Method	Description
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)
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)
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)
Map<CompositeSequence,Set<Gene>>	ArrayDesignDao.getGenesByCompositeSequence(Collection<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(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignDaoImpl.getGenesByCompositeSequence(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignService.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignService.getGenesByCompositeSequence(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignServiceImpl.getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	ArrayDesignServiceImpl.getGenesByCompositeSequence(ArrayDesign arrayDesign)
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)

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

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)

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

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
Slice<CompositeSequence>	ProcessedExpressionDataVectorService.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
List<CompositeSequence>	ProcessedExpressionDataVectorDao.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Only retrieve the design elements for a slice of vectors.
List<CompositeSequence>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)

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

Modifier and Type	Method	Description
int	RawAndProcessedExpressionDataVectorDao.removeByCompositeSequence(CompositeSequence cs)	Remove all raw and processed vectors for a given probe.
int	RawAndProcessedExpressionDataVectorDaoImpl.removeByCompositeSequence(CompositeSequence cs)
int	RawAndProcessedExpressionDataVectorService.removeByCompositeSequence(CompositeSequence cs)
int	RawAndProcessedExpressionDataVectorServiceImpl.removeByCompositeSequence(CompositeSequence cs)

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type CompositeSequence

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	RawExpressionDataVectorDao.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDaoImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorService.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorServiceImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)

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

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

Modifier and Type	Method	Description
CompositeSequence	CompositeSequenceService.create(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceDaoImpl.find(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceService.find(CompositeSequence compositeSequence)
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)
CompositeSequence	CompositeSequenceService.findOrCreate(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceService.thaw(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceServiceImpl.thaw(CompositeSequence compositeSequence)

Methods in ubic.gemma.persistence.service.expression.designElement that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
Collection<CompositeSequence>	CompositeSequenceDao.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceService.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	CompositeSequenceDao.findByBioSequenceName(String name)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByBioSequenceName(String name)
Collection<CompositeSequence>	CompositeSequenceService.findByBioSequenceName(String name)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByBioSequenceName(String name)
Collection<CompositeSequence>	CompositeSequenceDao.findByGene(Gene gene)
Slice<CompositeSequence>	CompositeSequenceDao.findByGene(Gene gene, int start, int limit)
Collection<CompositeSequence>	CompositeSequenceDao.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByGene(Gene gene)
Slice<CompositeSequence>	CompositeSequenceDaoImpl.findByGene(Gene gene, int start, int limit)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceService.findByGene(Gene gene)
Collection<CompositeSequence>	CompositeSequenceService.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByGene(Gene gene)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	CompositeSequenceDao.findByName(String name)
Collection<CompositeSequence>	CompositeSequenceDaoImpl.findByName(String name)
Collection<CompositeSequence>	CompositeSequenceService.findByName(String name)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByName(String name)
Collection<CompositeSequence>	CompositeSequenceService.findByNamesInArrayDesigns(Collection<String> compositeSequenceNames, Collection<ArrayDesign> arrayDesigns)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.findByNamesInArrayDesigns(Collection<String> compositeSequenceNames, Collection<ArrayDesign> arrayDesigns)	Checks to see if the CompositeSequence exists in any of the array designs.
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceDao.getGenes(Collection<CompositeSequence> compositeSequences)	Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceDaoImpl.getGenes(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceService.getGenes(Collection<CompositeSequence> sequences)	Given a Collection of composite sequences returns of map of a composite sequence to a collection of genes
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceServiceImpl.getGenes(Collection<CompositeSequence> sequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDao.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDaoImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceService.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceServiceImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<CompositeSequence>	CompositeSequenceService.load(Collection<Long> ids)
Collection<CompositeSequence>	CompositeSequenceService.thaw(Collection<CompositeSequence> compositeSequences)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.thaw(Collection<CompositeSequence> compositeSequences)

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

Modifier and Type	Method	Description
CompositeSequence	CompositeSequenceService.create(CompositeSequence compositeSequence)
protected CompositeSequenceValueObject	CompositeSequenceDaoImpl.doLoadValueObject(CompositeSequence entity)
CompositeSequence	CompositeSequenceDaoImpl.find(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceService.find(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceService.findOrCreate(CompositeSequence compositeSequence)
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)
Collection<Gene>	CompositeSequenceService.getGenes(CompositeSequence compositeSequence)
Slice<Gene>	CompositeSequenceService.getGenes(CompositeSequence compositeSequence, int offset, int limit)
Collection<Gene>	CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence)
Slice<Gene>	CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit)
protected void	CompositeSequenceDaoImpl.initializeCachedFilteringResult(CompositeSequence cachedEntity)
CompositeSequenceValueObject	CompositeSequenceService.loadValueObjectWithGeneMappingSummary(CompositeSequence cs)	Include gene mapping summary in the CompositeSequenceValueObject.
CompositeSequenceValueObject	CompositeSequenceServiceImpl.loadValueObjectWithGeneMappingSummary(CompositeSequence cs)
void	CompositeSequenceService.remove(CompositeSequence compositeSequence)
void	CompositeSequenceDao.thaw(CompositeSequence compositeSequence)
void	CompositeSequenceDaoImpl.thaw(CompositeSequence cs)
CompositeSequence	CompositeSequenceService.thaw(CompositeSequence compositeSequence)
CompositeSequence	CompositeSequenceServiceImpl.thaw(CompositeSequence compositeSequence)
void	CompositeSequenceService.update(CompositeSequence compositeSequence)

Method parameters in ubic.gemma.persistence.service.expression.designElement with type arguments of type CompositeSequence

Modifier and Type	Method	Description
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceDao.getGenes(Collection<CompositeSequence> compositeSequences)	Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceDaoImpl.getGenes(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceService.getGenes(Collection<CompositeSequence> sequences)	Given a Collection of composite sequences returns of map of a composite sequence to a collection of genes
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceServiceImpl.getGenes(Collection<CompositeSequence> sequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDao.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDaoImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceService.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceServiceImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	CompositeSequenceDao.getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	CompositeSequenceDaoImpl.getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	CompositeSequenceService.getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	CompositeSequenceServiceImpl.getRawSummary(Collection<CompositeSequence> compositeSequences)
void	CompositeSequenceServiceImpl.remove(Collection<CompositeSequence> sequencesToDelete)
void	CompositeSequenceDao.thaw(Collection<CompositeSequence> compositeSequences)
void	CompositeSequenceDaoImpl.thaw(Collection<CompositeSequence> compositeSequences)
Collection<CompositeSequence>	CompositeSequenceService.thaw(Collection<CompositeSequence> compositeSequences)
Collection<CompositeSequence>	CompositeSequenceServiceImpl.thaw(Collection<CompositeSequence> compositeSequences)

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

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type CompositeSequence

Modifier and Type	Method	Description
SingleCellExpressionDataVector	ExpressionExperimentDao.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	ExpressionExperimentDaoImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
SingleCellExpressionDataVector	SingleCellExpressionExperimentService.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)	Obtain a single single-cell vector without initializing cell IDs.
SingleCellExpressionDataVector	SingleCellExpressionExperimentServiceImpl.getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)

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

Methods in ubic.gemma.persistence.service.genome that return types with arguments of type CompositeSequence

Modifier and Type	Method	Description
Collection<CompositeSequence>	GeneDao.getCompositeSequences(Gene gene, boolean includeDummyProducts)	Get the composite sequences (e.g.
Collection<CompositeSequence>	GeneDao.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)	Get the composite sequences (e.g.
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequences(Gene gene, boolean includeDummyProducts)
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)
Collection<CompositeSequence>	GeneDao.getCompositeSequencesById(long id, boolean includeDummyProducts)
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequencesById(long id, boolean includeDummyProducts)	Gets all the CompositeSequences related to the gene identified by the given id.

Uses of CompositeSequence in ubic.gemma.persistence.service.genome.biosequence

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

Modifier and Type	Method	Description
BioSequence	BioSequenceDao.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceDaoImpl.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceService.findByCompositeSequence(CompositeSequence compositeSequence)
BioSequence	BioSequenceServiceImpl.findByCompositeSequence(CompositeSequence compositeSequence)

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

Methods in ubic.gemma.persistence.service.genome.gene that return types with arguments of type CompositeSequence

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

Uses of CompositeSequence in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static Collection<CompositeSequence>	CommonQueries.getCompositeSequences(Gene gene, Session session)	Given a gene, get all the composite sequences that map to it.
static Map<CompositeSequence,Collection<Gene>>	CommonQueries.getCs2GeneMap(Collection<Gene> genes, Collection<ArrayDesign> arrayDesigns, Session session)
static Map<CompositeSequence,Collection<Gene>>	CommonQueries.getCs2GeneMap(Collection<Gene> genes, Session session)

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

Modifier and Type	Method	Description
EntityUrlBuilder.ExpressionExperimentWebUrl	EntityUrlBuilder.ExpressionExperimentWebUrl.showSingleCellExpressionData(QuantitationType quantitationType, CompositeSequence designElement, List<BioAssay> assays, CellLevelCharacteristics cellLevelCharacteristics, Characteristic focusedCharacteristic)

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

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

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

Uses of CompositeSequence in ubic.gemma.web.controller.expression.designElement

Method parameters in ubic.gemma.web.controller.expression.designElement with type arguments of type CompositeSequence

Modifier and Type	Method	Description
Collection<GeneMappingSummary>	CompositeSequenceController.getGeneMappingSummary(EntityDelegator<CompositeSequence> csd)	Exposed for AJAX calls.

Uses of CompositeSequence in ubic.gemma.web.controller.expression.experiment

Methods in ubic.gemma.web.controller.expression.experiment that return CompositeSequence

Modifier and Type	Method	Description
CompositeSequence	SingleCellExpressionDataModel.getDesignElement()

Constructors in ubic.gemma.web.controller.expression.experiment with parameters of type CompositeSequence

Modifier	Constructor	Description
	SingleCellExpressionDataModel(ExpressionExperiment expressionExperiment, Collection<CellTypeAssignment> cellTypeAssignments, Collection<CellLevelCharacteristics> cellLevelCharacteristics, QuantitationType quantitationType, CompositeSequence designElement, Gene gene, Long[] assayIds, CellTypeAssignment cellTypeAssignment, CellLevelCharacteristics cellLevelCharacteristics1, Characteristic focusedCharacteristic, String keywords, String font)