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
ubic.gemma.core.analysis.preprocess.svd
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.search
ubic.gemma.core.search.source
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.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

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

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

Modifier and Type	Method	Description
Set<HitListSize>	DiffExAnalyzer.computeHitListSizes(Collection<DifferentialExpressionAnalysisResult> results, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)	Generate HitListSize entities that will be stored to count the number of diff.
Set<HitListSize>	LinearModelAnalyzer.computeHitListSizes(Collection<DifferentialExpressionAnalysisResult> results, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)
int	DiffExAnalyzer.getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult> resultList, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)	Utility method
int	LinearModelAnalyzer.getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult> resultList, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)
static DoubleMatrix<String,String>	LinearModelAnalyzer.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

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

Modifier and Type	Method	Description
Map<CompositeSequence,Double>	ExpressionDataMatrixBuilder.getRanksByMean()

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

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)

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

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

Modifier and Type	Method	Description
CompositeSequence	ExpressionDataMatrixRowElement.getDesignElement()
CompositeSequence	BaseExpressionDataMatrix.getDesignElementForRow(int index)
CompositeSequence	ExpressionDataMatrix.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>	BaseExpressionDataMatrix.getDesignElements()
List<CompositeSequence>	ExpressionDataMatrix.getDesignElements()	Obtain all the design elements in this data matrix.
DoubleMatrix<CompositeSequence,BioMaterial>	ExpressionDataDoubleMatrix.getMatrix()
Map<CompositeSequence,Double>	ExpressionDataDoubleMatrix.getRanks()
Collection<CompositeSequence>	ExpressionDataIntegerMatrix.getRowMap()
List<CompositeSequence>	ExpressionDataDoubleMatrix.getRowNames()

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

Modifier and Type	Method	Description
int	BaseExpressionDataMatrix.columns(CompositeSequence el)
int	ExpressionDataMatrix.columns(CompositeSequence el)	Number of columns that use the given design element.
Object	EmptyExpressionMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
Boolean	ExpressionDataBooleanMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
Double	ExpressionDataDoubleMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
Integer	ExpressionDataIntegerMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
Integer	ExpressionDataIntegerMatrix.get(CompositeSequence designElement, BioMaterial bioMaterial)
T	ExpressionDataMatrix.get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
String	ExpressionDataStringMatrix.get(CompositeSequence designElement, BioAssay bioAssay)
BioAssayDimension	BaseExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)
BioAssayDimension	ExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.
Object[]	EmptyExpressionMatrix.getRow(CompositeSequence designElement)
Boolean[]	ExpressionDataBooleanMatrix.getRow(CompositeSequence designElement)
Double[]	ExpressionDataDoubleMatrix.getRow(CompositeSequence designElement)
Integer[]	ExpressionDataIntegerMatrix.getRow(CompositeSequence designElement)
T[]	ExpressionDataMatrix.getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
String[]	ExpressionDataStringMatrix.getRow(CompositeSequence designElement)
int	BaseExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
int	ExpressionDataMatrix.getRowIndex(CompositeSequence designElement)
void	ExpressionDataDoubleMatrix.set(CompositeSequence designElement, BioAssay bioAssay, Double value)
void	ExpressionDataMatrixRowElement.setDesignElement(CompositeSequence designElement)

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

Modifier and Type	Method	Description
Object[][]	EmptyExpressionMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Boolean[][]	ExpressionDataBooleanMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Double[][]	ExpressionDataDoubleMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Integer[][]	ExpressionDataIntegerMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
T[][]	ExpressionDataMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)	Access a submatrix
String[][]	ExpressionDataStringMatrix.get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Object[][]	EmptyExpressionMatrix.getRows(List<CompositeSequence> designElements)
Boolean[][]	ExpressionDataBooleanMatrix.getRows(List<CompositeSequence> designElements)
Double[][]	ExpressionDataDoubleMatrix.getRows(List<CompositeSequence> designElements)
Integer[][]	ExpressionDataIntegerMatrix.getRows(List<CompositeSequence> designElements)
T[][]	ExpressionDataMatrix.getRows(List<CompositeSequence> designElements)	Access a submatrix
String[][]	ExpressionDataStringMatrix.getRows(List<CompositeSequence> designElements)
void	MatrixWriter.write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean orderByDesign)
void	MatrixWriter.write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)
void	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader)	Alternate method that uses annotations in string form (e.g., read from another file).
void	MatrixWriter.writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)

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

Constructor	Description
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<CompositeSequence> rowsToUse)	Create a matrix based on another one's selected rows.
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.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.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)

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)
Collection<SearchResult<CompositeSequence>>	DatabaseSearchSource.searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<CompositeSequence>>	HibernateSearchSource.searchCompositeSequence(SearchSettings settings)

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)

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

Constructor	Description
CompositeSequenceValueObject(CompositeSequence cs)

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,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 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)

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.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, ArrayDesign arrayDesign)
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	GeneDao.getCompositeSequencesById(long id)
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequencesById(long id)	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, ArrayDesign arrayDesign)	Returns a list of compositeSequences associated with the given gene and array design
Collection<CompositeSequence>	GeneServiceImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	GeneService.getCompositeSequencesById(Long id)
Collection<CompositeSequence>	GeneServiceImpl.getCompositeSequencesById(Long id)

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)

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.