Uses of Class
ubic.gemma.model.genome.Gene

Packages that use Gene

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix
ubic.gemma.core.goldenpath
ubic.gemma.core.image.aba
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.association
ubic.gemma.model.association.coexpression
ubic.gemma.model.association.phenotype
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.genome
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.association.coexpression
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.service.genome.sequenceAnalysis
ubic.gemma.persistence.util
ubic.gemma.rest.util.args
ubic.gemma.web.util

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

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

Modifier and Type	Method	Description
Set<Gene>	LinkAnalysis.getGenesTested()	Gene the genes that were tested, according to the rows that are currently in the dataMatrix (so call this after filtering!)
Map<CompositeSequence,Set<Gene>>	LinkAnalysis.getProbeToGeneMap()

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

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 Gene in ubic.gemma.core.analysis.expression.diff

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, double threshold, int limit)	Get the differential expression results for the given gene across all datasets.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)	Get differential expression for a gene, constrained to a specific set of factors.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionService.getDifferentialExpression(Gene gene, BioAssaySet ees, double threshold, int limit)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, double threshold, int limit)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)
Collection<DifferentialExpressionValueObject>	GeneDifferentialExpressionServiceImpl.getDifferentialExpression(Gene gene, BioAssaySet ee, double threshold, int limit)
DifferentialExpressionMetaAnalysisValueObject	GeneDifferentialExpressionService.getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)	Get the differential expression analysis results for the gene in the activeExperiments.
DifferentialExpressionMetaAnalysisValueObject	GeneDifferentialExpressionServiceImpl.getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)

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

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. ex probes at various preset thresholds, to avoid wasting time generating these counts on the fly later.
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)

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

Methods in ubic.gemma.core.analysis.sequence that return types with arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	CompositeSequenceMapSummary.getGenes()

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

Modifier and Type	Method	Description
static int	SequenceManipulation.getGeneExonOverlaps(String chromosome, String starts, String sizes, String strand, Gene gene)	Given a gene, find out how much of it overlaps with exons provided as starts and sizes.

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

Modifier and Type	Method	Description
void	CompositeSequenceMapSummary.setGenes(Collection<Gene> genes)

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

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

Modifier and Type	Method	Description
LinkedHashMap<Gene,Collection<CompositeSequence>>	CompositeSequenceGeneMapperService.getGene2ProbeMapByOfficialSymbols(Collection<String> officialSymbols, Collection<ArrayDesign> arrayDesigns)
DoubleMatrix<Gene,ExpressionExperiment>	ExpressionDataMatrixService.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
DoubleMatrix<Gene,ExpressionExperiment>	ExpressionDataMatrixServiceImpl.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
static Map<Long,Collection<Gene>>	ArrayDesignAnnotationServiceImpl.readAnnotationFile(ArrayDesign arrayDesign)

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResultListFileService.writeTsv(List<DifferentialExpressionAnalysisResult> payload, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
void	DifferentialExpressionAnalysisResultListFileServiceImpl.writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, Writer writer)

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

Modifier and Type	Method	Description
int	ArrayDesignAnnotationService.generateAnnotationFile(Writer writer, Collection<Gene> genes, Boolean useGO)	Generate an annotation for a list of genes, instead of probes.
int	ArrayDesignAnnotationServiceImpl.generateAnnotationFile(Writer writer, Collection<Gene> genes, Boolean useGO)
DoubleMatrix<Gene,ExpressionExperiment>	ExpressionDataMatrixService.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
DoubleMatrix<Gene,ExpressionExperiment>	ExpressionDataMatrixServiceImpl.getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
void	ExpressionAnalysisResultSetFileService.writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> result2Genes, Writer writer)	Write the analysis result set with result-to-gene mappings.
void	ExpressionAnalysisResultSetFileServiceImpl.writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> resultId2Genes, Writer appendable)

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

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

Modifier and Type	Method	Description
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)

Uses of Gene in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath that return Gene

Modifier and Type	Method	Description
Gene	GoldenPathSequenceAnalysis.findClosestGene(String chromosome, Long queryStart, Long queryEnd, String strand, int maxWindow)	Given a location, find the nearest gene on the same strand, including only "known", "refseq" or "ensembl" transcripts.

Methods in ubic.gemma.core.goldenpath that return types with arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	GoldenPathSequenceAnalysis.findESTs(String chromosome, Long regionStart, Long regionEnd, String strand)	Check to see if there are ESTs that overlap with this region.
Collection<Gene>	GoldenPathSequenceAnalysis.findRNAs(String chromosome, Long regionStart, Long regionEnd, String strand)	Check to see if there are mRNAs that overlap with this region.

Uses of Gene in ubic.gemma.core.image.aba

Methods in ubic.gemma.core.image.aba with parameters of type Gene

Modifier and Type	Method	Description
AbaGene	AllenBrainAtlasService.getGene(Gene gene)
AbaGene	AllenBrainAtlasServiceImpl.getGene(Gene gene)	Given a gene too look for for will return the corresponding abaGene (useful for finding images)
String	AllenBrainAtlasService.getGeneUrl(Gene gene)	Given a Gemma gene object returns an allen brain atlas gene URL
String	AllenBrainAtlasServiceImpl.getGeneUrl(Gene gene)
Collection<ImageSeries>	AllenBrainAtlasService.getSagittalImageSeries(Gene gene)	Given a Gene, returns all the image series that contain sagittal images for the given gene.
Collection<ImageSeries>	AllenBrainAtlasServiceImpl.getSagittalImageSeries(Gene gene)

Uses of Gene in ubic.gemma.core.loader.genome.gene.ncbi

Methods in ubic.gemma.core.loader.genome.gene.ncbi that return Gene

Modifier and Type	Method	Description
Gene	NcbiGeneConverter.convert(NCBIGeneInfo info)
Gene	NcbiGeneConverter.convert(NcbiGeneData data)

Methods in ubic.gemma.core.loader.genome.gene.ncbi with parameters of type Gene

Modifier and Type	Method	Description
Collection<GeneProduct>	NcbiGeneConverter.convert(NCBIGene2Accession acc, Gene gene)

Uses of Gene in ubic.gemma.core.loader.genome.gene.ncbi.homology

Methods in ubic.gemma.core.loader.genome.gene.ncbi.homology that return Gene

Modifier and Type	Method	Description
Gene	HomologeneService.getHomologue(Gene gene, Taxon taxon)
Gene	HomologeneServiceImpl.getHomologue(Gene gene, Taxon taxon)

Methods in ubic.gemma.core.loader.genome.gene.ncbi.homology that return types with arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	HomologeneService.getHomologues(Gene gene)
Collection<Gene>	HomologeneServiceImpl.getHomologues(Gene gene)

Methods in ubic.gemma.core.loader.genome.gene.ncbi.homology with parameters of type Gene

Modifier and Type	Method	Description
Gene	HomologeneService.getHomologue(Gene gene, Taxon taxon)
Gene	HomologeneServiceImpl.getHomologue(Gene gene, Taxon taxon)
Collection<Gene>	HomologeneService.getHomologues(Gene gene)
Collection<Gene>	HomologeneServiceImpl.getHomologues(Gene gene)

Uses of Gene in ubic.gemma.core.ontology

Methods in ubic.gemma.core.ontology with parameters of type Gene

Modifier and Type	Method	Description
Double	GoMetric.computeMatrixSimilarity(Gene gene1, Gene gene2, DoubleMatrix<Long,String> gene2TermMatrix, GoMetric.Metric metric)
Double	GoMetricImpl.computeMatrixSimilarity(Gene gene1, Gene gene2, DoubleMatrix<Long,String> gene2TermMatrix, GoMetric.Metric metric)
Double	GoMetric.computeMaxSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	GoMetricImpl.computeMaxSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	GoMetric.computeSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	GoMetricImpl.computeSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	GoMetric.computeSimpleOverlap(Gene g, Gene coexpG, Map<Long,Collection<String>> geneGoMap)
Double	GoMetricImpl.computeSimpleOverlap(Gene g, Gene coexpG, Map<Long,Collection<String>> geneGoMap)

Method parameters in ubic.gemma.core.ontology with type arguments of type Gene

Modifier and Type	Method	Description
Double	GoMetric.computeMergedOverlap(List<Gene> sameGenes1, List<Gene> sameGenes2, Map<Long,Collection<String>> geneGoMap)
Double	GoMetricImpl.computeMergedOverlap(List<Gene> sameGenes1, List<Gene> sameGenes2, Map<Long,Collection<String>> geneGoMap)	Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs.

Uses of Gene in ubic.gemma.core.ontology.providers

Methods in ubic.gemma.core.ontology.providers that return types with arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	GeneOntologyService.getGenes(String goId, Taxon taxon)	Find genes for a given GO term by GO ID.
Collection<Gene>	GeneOntologyService.getGenes(OntologyTerm goTerm, Taxon taxon)	Find genes for a given of GO term.
Collection<Gene>	GeneOntologyServiceImpl.getGenes(String goId, Taxon taxon)
Collection<Gene>	GeneOntologyServiceImpl.getGenes(OntologyTerm term, Taxon taxon)

Methods in ubic.gemma.core.ontology.providers with parameters of type Gene

Modifier and Type	Method	Description
Map<Long,Collection<OntologyTerm>>	GeneOntologyService.calculateGoTermOverlap(Gene queryGene, Collection<Long> geneIds)	Given a query Gene, and a collection of gene ids calculates the go term overlap for each pair of queryGene and gene in the given collection.
Collection<OntologyTerm>	GeneOntologyService.calculateGoTermOverlap(Gene queryGene1, Gene queryGene2)
Map<Long,Collection<OntologyTerm>>	GeneOntologyServiceImpl.calculateGoTermOverlap(Gene queryGene, Collection<Long> geneIds)
Collection<OntologyTerm>	GeneOntologyServiceImpl.calculateGoTermOverlap(Gene queryGene1, Gene queryGene2)
Collection<OntologyTerm>	GeneOntologyService.getGOTerms(Gene gene)
Collection<OntologyTerm>	GeneOntologyService.getGOTerms(Gene gene, boolean includePartOf, GeneOntologyServiceImpl.GOAspect goAspect)	Get all GO terms for a gene, including parents of terms via is-a relationships; and optionally also parents via part-of relationships.
Collection<OntologyTerm>	GeneOntologyServiceImpl.getGOTerms(Gene gene)
Collection<OntologyTerm>	GeneOntologyServiceImpl.getGOTerms(Gene gene, boolean includePartOf, GeneOntologyServiceImpl.GOAspect goAspect)
List<GeneOntologyTermValueObject>	GeneOntologyService.getValueObjects(Gene gene)	Returns GO Terms VOs for the given Gene.
List<GeneOntologyTermValueObject>	GeneOntologyServiceImpl.getValueObjects(Gene gene)

Uses of Gene in ubic.gemma.core.search

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

Modifier and Type	Method	Description
default Collection<SearchResult<Gene>>	SearchSource.searchGene(SearchSettings settings)

Methods in ubic.gemma.core.search with parameters of type Gene

Modifier and Type	Method	Description
Collection<GeneSet>	GeneSetSearch.findByGene(Gene gene)
Collection<GeneSet>	GeneSetSearchImpl.findByGene(Gene gene)

Method parameters in ubic.gemma.core.search with type arguments of type Gene

Modifier and Type	Method	Description
default Collection<SearchResult<?>>	SearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead

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

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

Modifier and Type	Method	Description
Collection<SearchResult<Gene>>	CompositeSearchSource.searchGene(SearchSettings settings)
Collection<SearchResult<Gene>>	DatabaseSearchSource.searchGene(SearchSettings settings)	Search the DB for genes that exactly match the given search string searches geneProducts, gene and bioSequence tables
Collection<SearchResult<Gene>>	GeneOntologySearchSource.searchGene(SearchSettings settings)
Collection<SearchResult<Gene>>	HibernateSearchSource.searchGene(SearchSettings settings)

Method parameters in ubic.gemma.core.search.source with type arguments of type Gene

Modifier and Type	Method	Description
Collection<SearchResult<?>>	CompositeSearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated.
Collection<SearchResult<?>>	DatabaseSearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)

Uses of Gene in ubic.gemma.model.analysis.expression.coexpression

Constructors in ubic.gemma.model.analysis.expression.coexpression with parameters of type Gene

Constructor	Description
HumanCoexpressionSupportDetailsImpl(Gene firstGene, Gene secondGene, Boolean isPositive)
MouseCoexpressionSupportDetailsImpl(Gene firstGene, Gene secondGene, Boolean isPositive)
OtherCoexpressionSupportDetailsImpl(Gene firstGene, Gene secondGene, Boolean isPositive)
RatCoexpressionSupportDetailsImpl(Gene firstGene, Gene secondGene, Boolean isPositive)
SupportDetails(Gene firstGene, Gene secondGene, Boolean isPositive)	Note that the gene information and isPositive is only used for bookkeeping during creation; it is not part of the persistent entity.

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

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

Modifier and Type	Method	Description
Gene	GeneDifferentialExpressionMetaAnalysisResult.getGene()

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

Modifier and Type	Method	Description
void	GeneDifferentialExpressionMetaAnalysisResult.setGene(Gene gene)

Constructor parameters in ubic.gemma.model.analysis.expression.diff with type arguments of type Gene

Constructor	Description
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet, boolean includeFactorValuesInContrasts, Map<Long,List<Gene>> result2Genes, boolean includeTaxonInGenes)	Create an expression analysis result set VO with all its associated results.
DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult result, boolean includeFactorValuesInContrasts, List<Gene> genes, boolean includeTaxonInGenes)

Uses of Gene in ubic.gemma.model.association

Methods in ubic.gemma.model.association that return Gene

Modifier and Type	Method	Description
Gene	Gene2GeneAssociation.getFirstGene()
Gene	Gene2GOAssociation.getGene()
Gene	Gene2GeneAssociation.getSecondGene()

Methods in ubic.gemma.model.association with parameters of type Gene

Modifier and Type	Method	Description
static Gene2GOAssociation	Gene2GOAssociation.Factory.newInstance(Gene gene, Characteristic ontologyEntry, GOEvidenceCode evidenceCode)

Uses of Gene in ubic.gemma.model.association.coexpression

Methods in ubic.gemma.model.association.coexpression with parameters of type Gene

Modifier and Type	Method	Description
static GeneCoexpressionNodeDegree	GeneCoexpressionNodeDegree.Factory.newInstance(Gene g)

Uses of Gene in ubic.gemma.model.association.phenotype

Methods in ubic.gemma.model.association.phenotype that return Gene

Modifier and Type	Method	Description
Gene	PhenotypeAssociation.getGene()	Deprecated.

Methods in ubic.gemma.model.association.phenotype with parameters of type Gene

Modifier and Type	Method	Description
void	PhenotypeAssociation.setGene(Gene gene)	Deprecated.

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

Constructor parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type Gene

Constructor	Description
ExperimentExpressionLevelsValueObject(long datasetId, Map<Gene,List<DoubleVectorValueObject>> vectorsPerGene, boolean keepGeneNonSpecific, String conslidationMode)

Uses of Gene in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return Gene

Modifier and Type	Method	Description
static Gene	Gene.Factory.newInstance()

Uses of Gene in ubic.gemma.model.genome.gene

Methods in ubic.gemma.model.genome.gene that return Gene

Modifier and Type	Method	Description
Gene	GeneProduct.getGene()
Gene	GeneSetMember.getGene()

Methods in ubic.gemma.model.genome.gene with parameters of type Gene

Modifier and Type	Method	Description
static GeneSetMember	GeneSet.containsGene(Gene g, GeneSet gs)
static GeneValueObject	GeneValueObject.convert2ValueObject(Gene gene)	Converts a Gene to a GeneValueObject
static GeneSetMember	GeneSetMember.Factory.newInstance(Double score, Gene gene)
void	GeneProduct.setGene(Gene gene)
void	GeneSetMember.setGene(Gene gene)

Constructors in ubic.gemma.model.genome.gene with parameters of type Gene

Constructor	Description
GeneValueObject(Gene gene)
GeneValueObject(Gene gene, boolean includeTaxon)

Uses of Gene in ubic.gemma.model.genome.gene.phenotype.valueObject

Constructors in ubic.gemma.model.genome.gene.phenotype.valueObject with parameters of type Gene

Constructor	Description
GeneEvidenceValueObject(Gene gene, Collection<EvidenceValueObject<? extends PhenotypeAssociation>> evidence)	Deprecated.

Uses of Gene in ubic.gemma.persistence.persister

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

Modifier and Type	Method	Description
protected Gene	GenomePersister.persistGene(Gene gene, AbstractPersister.Caches caches)

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

Modifier and Type	Method	Description
protected Gene	GenomePersister.persistGene(Gene gene, AbstractPersister.Caches caches)

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

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type Gene

Modifier and Type	Method	Description
Map<Long,List<Gene>>	ExpressionAnalysisResultSetService.loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)
Map<Long,List<Gene>>	ExpressionAnalysisResultSetServiceImpl.loadResultIdToGenesMap(ExpressionAnalysisResultSet resultSet)
Map<Long,List<Gene>>	ExpressionAnalysisResultSetDao.loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)	Load a DifferentialExpressionAnalysisResult to Gene multi-map.
Map<Long,List<Gene>>	ExpressionAnalysisResultSetDaoImpl.loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type Gene

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.find(Gene gene, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, Collection<Long> experimentsAnalyzed)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultService.find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultServiceImpl.find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGene(Gene gene)	Find differential expression results for a given gene, grouped by experiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecific, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecific, boolean initializeFactorValues)
Collection<BioAssaySet>	DifferentialExpressionAnalysisDao.findExperimentsWithAnalyses(Gene gene)
Collection<BioAssaySet>	DifferentialExpressionAnalysisService.findExperimentsWithAnalyses(Gene gene)
Collection<BioAssaySet>	DifferentialExpressionAnalysisServiceImpl.findExperimentsWithAnalyses(Gene gene)

Uses of Gene in ubic.gemma.persistence.service.association

Methods in ubic.gemma.persistence.service.association that return types with arguments of type Gene

Modifier and Type	Method	Description
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDao.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationServiceImpl.findByGenes(Collection<Gene> genes)
Collection<Gene>	Gene2GOAssociationDao.findByGoTermUris(Collection<String> uris)
Collection<Gene>	Gene2GOAssociationDao.findByGoTermUris(Collection<String> uris, Taxon taxon)
Collection<Gene>	Gene2GOAssociationDaoImpl.findByGoTermUris(Collection<String> uris)
Collection<Gene>	Gene2GOAssociationDaoImpl.findByGoTermUris(Collection<String> uris, Taxon taxon)
Collection<Gene>	Gene2GOAssociationService.findByGOTermUris(Collection<String> uris, Taxon taxon)	Find all the genes that match any of the terms.
Collection<Gene>	Gene2GOAssociationServiceImpl.findByGOTermUris(Collection<String> uris, Taxon taxon)
Map<Taxon,Collection<Gene>>	Gene2GOAssociationDao.findByGoTermUrisPerTaxon(Collection<String> uris)
Map<Taxon,Collection<Gene>>	Gene2GOAssociationDaoImpl.findByGoTermUrisPerTaxon(Collection<String> uris)
Map<Taxon,Collection<Gene>>	Gene2GOAssociationService.findByGOTermUrisPerTaxon(Collection<String> uris)	Find all genes associated with a given set of GO terms, grouped by taxon.
Map<Taxon,Collection<Gene>>	Gene2GOAssociationServiceImpl.findByGOTermUrisPerTaxon(Collection<String> uris)

Methods in ubic.gemma.persistence.service.association with parameters of type Gene

Modifier and Type	Method	Description
Collection<Gene2GOAssociation>	Gene2GOAssociationDao.findAssociationByGene(Gene gene)
Collection<Gene2GOAssociation>	Gene2GOAssociationDaoImpl.findAssociationByGene(Gene gene)
Collection<Gene2GOAssociation>	Gene2GOAssociationService.findAssociationByGene(Gene gene)
Collection<Gene2GOAssociation>	Gene2GOAssociationServiceImpl.findAssociationByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationDao.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationDaoImpl.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationService.findByGene(Gene gene)
Collection<Characteristic>	Gene2GOAssociationServiceImpl.findByGene(Gene gene)

Method parameters in ubic.gemma.persistence.service.association with type arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene2GOAssociation>	Gene2GOAssociationDao.findAssociationByGenes(Collection<Gene> genes)
Collection<Gene2GOAssociation>	Gene2GOAssociationDaoImpl.findAssociationByGenes(Collection<Gene> genes)
Collection<Gene2GOAssociation>	Gene2GOAssociationService.findAssociationByGenes(Collection<Gene> genes)
Collection<Gene2GOAssociation>	Gene2GOAssociationServiceImpl.findAssociationByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDao.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<Characteristic>>	Gene2GOAssociationServiceImpl.findByGenes(Collection<Gene> genes)

Uses of Gene in ubic.gemma.persistence.service.association.coexpression

Methods in ubic.gemma.persistence.service.association.coexpression that return types with arguments of type Gene

Modifier and Type	Method	Description
Map<Gene,Integer>	CoexpressionDao.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionDaoImpl.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionService.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionServiceImpl.countOldLinks(Collection<Gene> genes)

Methods in ubic.gemma.persistence.service.association.coexpression with parameters of type Gene

Modifier and Type	Method	Description
Integer	CoexpressionDao.countLinks(Gene gene, BioAssaySet ee)
Integer	CoexpressionDaoImpl.countLinks(Gene gene, BioAssaySet ee)
Integer	CoexpressionService.countLinks(BioAssaySet ee, Gene gene)
Integer	CoexpressionServiceImpl.countLinks(BioAssaySet ee, Gene gene)
SupportDetails	LinkCreator.createSupportDetails(Gene g1, Gene g2, Boolean isPositive)
List<CoexpressionValueObject>	CoexpressionDao.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for a gene that are common to all the given datasets.
List<CoexpressionValueObject>	CoexpressionDaoImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)
List<CoexpressionValueObject>	CoexpressionService.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find links which are common to all of the given data sets.
List<CoexpressionValueObject>	CoexpressionService.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.
List<CoexpressionValueObject>	CoexpressionServiceImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)
List<CoexpressionValueObject>	CoexpressionServiceImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int stringency, int maxResults, boolean quick)
GeneCoexpressionNodeDegree	CoexpressionNodeDegreeDao.findOrCreate(Gene gene)
GeneCoexpressionNodeDegree	CoexpressionNodeDegreeDaoImpl.findOrCreate(Gene gene)
GeneCoexpressionNodeDegreeValueObject	CoexpressionService.getNodeDegree(Gene g)
GeneCoexpressionNodeDegreeValueObject	CoexpressionServiceImpl.getNodeDegree(Gene g)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionDao.initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionDaoImpl.initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionService.initializeLinksFromOldData(Gene gene, Map<Long,Gene> idMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionServiceImpl.initializeLinksFromOldData(Gene g, Map<Long,Gene> idMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
int	CoexpressionDao.queryAndCache(Gene gene)
int	CoexpressionDaoImpl.queryAndCache(Gene gene)
GeneCoexpressionNodeDegreeValueObject	CoexpressionDao.updateNodeDegree(Gene gene, GeneCoexpressionNodeDegree nd)	This is a maintenance method.
GeneCoexpressionNodeDegreeValueObject	CoexpressionDaoImpl.updateNodeDegree(Gene g, GeneCoexpressionNodeDegree nd)

Method parameters in ubic.gemma.persistence.service.association.coexpression with type arguments of type Gene

Modifier and Type	Method	Description
Map<Gene,Integer>	CoexpressionDao.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionDaoImpl.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionService.countOldLinks(Collection<Gene> genes)
Map<Gene,Integer>	CoexpressionServiceImpl.countOldLinks(Collection<Gene> genes)
void	CoexpressionDao.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> p2plinks, LinkCreator c, Set<Gene> genesTested)
void	CoexpressionDaoImpl.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)
void	CoexpressionService.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> geesTested)	Maintenance method.
void	CoexpressionServiceImpl.createOrUpdate(BioAssaySet bioAssaySet, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionDao.initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionDaoImpl.initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionService.initializeLinksFromOldData(Gene gene, Map<Long,Gene> idMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
Map<SupportDetails,Gene2GeneCoexpression>	CoexpressionServiceImpl.initializeLinksFromOldData(Gene g, Map<Long,Gene> idMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)

Constructors in ubic.gemma.persistence.service.association.coexpression with parameters of type Gene

Constructor	Description
NonPersistentNonOrderedCoexpLink(Gene g1, Gene g2, boolean b)

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

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

Modifier and Type	Method	Description
Collection<Gene>	ArrayDesignDao.getGenes(ArrayDesign arrayDesign)
Collection<Gene>	ArrayDesignDaoImpl.getGenes(ArrayDesign arrayDesign)
Collection<Gene>	ArrayDesignService.getGenes(ArrayDesign arrayDesign)	Obtain all the genes associated to the platform.
Collection<Gene>	ArrayDesignServiceImpl.getGenes(ArrayDesign arrayDesign)

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

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

Modifier and Type	Method	Description
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	ProcessedExpressionDataVectorDao.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	ProcessedExpressionDataVectorDao.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	ProcessedExpressionDataVectorDaoImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	ProcessedExpressionDataVectorDaoImpl.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	ProcessedExpressionDataVectorService.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	ProcessedExpressionDataVectorServiceImpl.getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)

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

Modifier and Type	Method	Description
Map<Gene,Collection<Double>>	ProcessedExpressionDataVectorDao.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	ProcessedExpressionDataVectorDaoImpl.getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)

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

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

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
Slice<Gene>	CompositeSequenceDao.getGenes(CompositeSequence compositeSequence, int offset, int limit)	given a composite sequence returns a collection of genes
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceDaoImpl.getGenes(Collection<CompositeSequence> compositeSequences)
Slice<Gene>	CompositeSequenceDaoImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit)
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
Collection<Gene>	CompositeSequenceService.getGenes(CompositeSequence compositeSequence)
Slice<Gene>	CompositeSequenceService.getGenes(CompositeSequence compositeSequence, int offset, int limit)
Map<CompositeSequence,Collection<Gene>>	CompositeSequenceServiceImpl.getGenes(Collection<CompositeSequence> sequences)
Collection<Gene>	CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence)
Slice<Gene>	CompositeSequenceServiceImpl.getGenes(CompositeSequence compositeSequence, int offset, int limit)

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

Modifier and Type	Method	Description
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)
Slice<CompositeSequenceValueObject>	CompositeSequenceService.loadValueObjectsForGene(Gene gene, int start, int limit)
Slice<CompositeSequenceValueObject>	CompositeSequenceServiceImpl.loadValueObjectsForGene(Gene gene, int start, int limit)

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

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

Modifier and Type	Method	Description
Collection<Gene>	ExpressionExperimentDao.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)	Obtain genes used by the processed vectors of this dataset.
Collection<Gene>	ExpressionExperimentDaoImpl.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)
Collection<Gene>	ExpressionExperimentService.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)	Retrieve the genes used by the preferred vectors of this experiment.
Collection<Gene>	ExpressionExperimentServiceImpl.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)

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

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByExpressedGene(Gene gene, Double rank)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByExpressedGene(Gene gene, double rank)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByGene(Gene gene)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByGene(Gene gene)

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

Methods in ubic.gemma.persistence.service.genome that return Gene

Modifier and Type	Method	Description
Gene	GeneDaoImpl.find(Gene gene)
Gene	GeneDao.findByAccession(String accession, ExternalDatabase source)
Gene	GeneDaoImpl.findByAccession(String accession, ExternalDatabase source)
Gene	GeneDao.findByEnsemblId(String exactString)
Gene	GeneDaoImpl.findByEnsemblId(String id)
Gene	GeneDao.findByNcbiId(Integer accession)
Gene	GeneDaoImpl.findByNcbiId(Integer ncbiId)
Gene	GeneDao.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneDaoImpl.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneDao.thaw(Gene gene)
Gene	GeneDaoImpl.thaw(Gene gene)
Gene	GeneDao.thawAliases(Gene gene)
Gene	GeneDaoImpl.thawAliases(Gene gene)	Only thaw the Aliases, very light version
Gene	GeneDao.thawLite(Gene gene)
Gene	GeneDaoImpl.thawLite(Gene gene)
Gene	GeneDao.thawLiter(Gene gene)
Gene	GeneDaoImpl.thawLiter(Gene gene)

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

Modifier and Type	Method	Description
Collection<Gene>	GeneDao.find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Collection<Gene>	GeneDaoImpl.find(PhysicalLocation physicalLocation)
Collection<Gene>	GeneDao.findByAlias(String search)	Locate genes that match the given alias string
Collection<Gene>	GeneDaoImpl.findByAlias(String search)	Gets all the genes referred to by the alias defined by the search string.
Map<Integer,Gene>	GeneDao.findByNcbiIds(Collection<Integer> ncbiIds)	Quickly load exact matches.
Map<Integer,Gene>	GeneDaoImpl.findByNcbiIds(Collection<Integer> ncbiIds)
Collection<Gene>	GeneDao.findByOfficialName(String officialName)
Collection<Gene>	GeneDaoImpl.findByOfficialName(String officialName)
Collection<Gene>	GeneDao.findByOfficialNameInexact(String officialName)
Collection<Gene>	GeneDaoImpl.findByOfficialNameInexact(String officialName)
Collection<Gene>	GeneDao.findByOfficialSymbol(String officialSymbol)
Collection<Gene>	GeneDaoImpl.findByOfficialSymbol(String officialSymbol)
Collection<Gene>	GeneDao.findByOfficialSymbolInexact(String officialSymbol)
Collection<Gene>	GeneDaoImpl.findByOfficialSymbolInexact(String officialSymbol)
Map<String,Gene>	GeneDao.findByOfficialSymbols(Collection<String> query, Long taxonId)	Quickly load exact matches.
Map<String,Gene>	GeneDaoImpl.findByOfficialSymbols(Collection<String> query, Long taxonId)
Collection<Gene>	GeneDao.findByPhysicalLocation(PhysicalLocation location)	Deprecated.
Collection<Gene>	GeneDaoImpl.findByPhysicalLocation(PhysicalLocation location)
Collection<Gene>	GeneDao.getMicroRnaByTaxon(Taxon taxon)
Collection<Gene>	GeneDaoImpl.getMicroRnaByTaxon(Taxon taxon)
Collection<Gene>	GeneDao.loadKnownGenes(Taxon taxon)
Collection<Gene>	GeneDaoImpl.loadKnownGenes(Taxon taxon)
List<Gene>	GeneDao.loadThawed(Collection<Long> ids)
List<Gene>	GeneDaoImpl.loadThawed(Collection<Long> ids)
Collection<Gene>	GeneDao.loadThawedLiter(Collection<Long> ids)
Collection<Gene>	GeneDaoImpl.loadThawedLiter(Collection<Long> ids)
Collection<Gene>	GeneDao.thawLite(Collection<Gene> genes)
Collection<Gene>	GeneDaoImpl.thawLite(Collection<Gene> genes)

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

Modifier and Type	Method	Description
protected GeneValueObject	GeneDaoImpl.doLoadValueObject(Gene entity)
Gene	GeneDaoImpl.find(Gene gene)
Collection<CompositeSequence>	GeneDao.getCompositeSequences(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	GeneDaoImpl.getCompositeSequences(Gene gene, ArrayDesign arrayDesign)
protected void	GeneDaoImpl.initializeCachedFilteringResult(Gene entity)
void	GeneDaoImpl.remove(Gene gene)
Gene	GeneDao.thaw(Gene gene)
Gene	GeneDaoImpl.thaw(Gene gene)
Gene	GeneDao.thawAliases(Gene gene)
Gene	GeneDaoImpl.thawAliases(Gene gene)	Only thaw the Aliases, very light version
Gene	GeneDao.thawLite(Gene gene)
Gene	GeneDaoImpl.thawLite(Gene gene)
Gene	GeneDao.thawLiter(Gene gene)
Gene	GeneDaoImpl.thawLiter(Gene gene)

Method parameters in ubic.gemma.persistence.service.genome with type arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	GeneDao.thawLite(Collection<Gene> genes)
Collection<Gene>	GeneDaoImpl.thawLite(Collection<Gene> genes)

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

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

Modifier and Type	Method	Description
Map<Gene,Collection<BioSequence>>	BioSequenceDao.findByGenes(Collection<Gene> genes)	Returns matching biosequences for the given genes in a Map (gene to biosequences).
Map<Gene,Collection<BioSequence>>	BioSequenceDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceServiceImpl.findByGenes(Collection<Gene> genes)
Collection<Gene>	BioSequenceDao.getGenesByAccession(String search)
Collection<Gene>	BioSequenceDaoImpl.getGenesByAccession(String search)
Collection<Gene>	BioSequenceService.getGenesByAccession(String search)
Collection<Gene>	BioSequenceServiceImpl.getGenesByAccession(String search)
Collection<Gene>	BioSequenceDao.getGenesByName(String search)	For a biosequence name, get the genes
Collection<Gene>	BioSequenceDaoImpl.getGenesByName(String search)
Collection<Gene>	BioSequenceService.getGenesByName(String search)
Collection<Gene>	BioSequenceServiceImpl.getGenesByName(String search)

Method parameters in ubic.gemma.persistence.service.genome.biosequence with type arguments of type Gene

Modifier and Type	Method	Description
Map<Gene,Collection<BioSequence>>	BioSequenceDao.findByGenes(Collection<Gene> genes)	Returns matching biosequences for the given genes in a Map (gene to biosequences).
Map<Gene,Collection<BioSequence>>	BioSequenceDaoImpl.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceService.findByGenes(Collection<Gene> genes)
Map<Gene,Collection<BioSequence>>	BioSequenceServiceImpl.findByGenes(Collection<Gene> genes)

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

Methods in ubic.gemma.persistence.service.genome.gene that return Gene

Modifier and Type	Method	Description
Gene	GeneService.create(Gene gene)
Gene	GeneService.findByAccession(String accession, ExternalDatabase source)
Gene	GeneServiceImpl.findByAccession(String accession, ExternalDatabase source)
Gene	GeneService.findByEnsemblId(String exactString)	Searches for a gene based on its ensembl ID.
Gene	GeneServiceImpl.findByEnsemblId(String exactString)
Gene	GeneService.findByNCBIId(Integer accession)
Gene	GeneServiceImpl.findByNCBIId(Integer accession)
Gene	GeneService.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneServiceImpl.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneService.thaw(Gene gene)
Gene	GeneServiceImpl.thaw(Gene gene)
Gene	GeneService.thawAliases(Gene gene)
Gene	GeneServiceImpl.thawAliases(Gene gene)
Gene	GeneService.thawLite(Gene gene)
Gene	GeneServiceImpl.thawLite(Gene gene)
Gene	GeneService.thawLiter(Gene gene)
Gene	GeneServiceImpl.thawLiter(Gene gene)

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

Modifier and Type	Method	Description
Collection<Gene>	GeneService.find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Collection<Gene>	GeneServiceImpl.find(PhysicalLocation physicalLocation)
Collection<Gene>	GeneService.findByAlias(String search)
Collection<Gene>	GeneServiceImpl.findByAlias(String search)
Collection<Gene>	GeneService.findByOfficialName(String officialName)
Collection<Gene>	GeneServiceImpl.findByOfficialName(String officialName)
Collection<Gene>	GeneService.findByOfficialNameInexact(String officialName)
Collection<Gene>	GeneServiceImpl.findByOfficialNameInexact(String officialName)
Collection<Gene>	GeneService.findByOfficialSymbol(String officialSymbol)
Collection<Gene>	GeneServiceImpl.findByOfficialSymbol(String officialSymbol)
Collection<Gene>	GeneService.findByOfficialSymbolInexact(String officialSymbol)
Collection<Gene>	GeneServiceImpl.findByOfficialSymbolInexact(String officialSymbol)
Collection<Gene>	GeneProductDao.getGenesByName(String search)
Collection<Gene>	GeneProductDaoImpl.getGenesByName(String search)
Collection<Gene>	GeneProductService.getGenesByName(String search)
Collection<Gene>	GeneProductServiceImpl.getGenesByName(String search)
Collection<Gene>	GeneProductDao.getGenesByNcbiId(String search)
Collection<Gene>	GeneProductDaoImpl.getGenesByNcbiId(String search)
Collection<Gene>	GeneProductService.getGenesByNcbiId(String search)
Collection<Gene>	GeneProductServiceImpl.getGenesByNcbiId(String search)
Collection<Gene>	GeneSearchService.getGOGroupGenes(String goQuery, Taxon taxon)
Collection<Gene>	GeneSearchServiceImpl.getGOGroupGenes(String goQuery, Taxon taxon)
Collection<Gene>	GeneService.loadAll(Taxon taxon)
Collection<Gene>	GeneServiceImpl.loadAll(Taxon taxon)
Collection<Gene>	GeneService.loadMicroRNAs(Taxon taxon)
Collection<Gene>	GeneServiceImpl.loadMicroRNAs(Taxon taxon)
Collection<Gene>	GeneService.loadThawed(Collection<Long> ids)	Load with objects already thawed.
Collection<Gene>	GeneServiceImpl.loadThawed(Collection<Long> ids)
Collection<Gene>	GeneService.loadThawedLiter(Collection<Long> ids)
Collection<Gene>	GeneServiceImpl.loadThawedLiter(Collection<Long> ids)
Collection<Gene>	GeneService.thawLite(Collection<Gene> genes)
Collection<Gene>	GeneServiceImpl.thawLite(Collection<Gene> genes)

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

Modifier and Type	Method	Description
Gene	GeneService.create(Gene gene)
Collection<GeneSet>	GeneSetDao.findByGene(Gene gene)
Collection<GeneSet>	GeneSetDaoImpl.findByGene(Gene gene)
Collection<GeneSet>	GeneSetService.findByGene(Gene gene)	Return all sets that contain the given gene.
Collection<GeneSet>	GeneSetServiceImpl.findByGene(Gene gene)
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)
List<PhysicalLocationValueObject>	GeneService.getPhysicalLocationsValueObjects(Gene gene)
List<PhysicalLocationValueObject>	GeneServiceImpl.getPhysicalLocationsValueObjects(Gene gene)
void	GeneService.remove(Gene gene)
Gene	GeneService.thaw(Gene gene)
Gene	GeneServiceImpl.thaw(Gene gene)
Gene	GeneService.thawAliases(Gene gene)
Gene	GeneServiceImpl.thawAliases(Gene gene)
Gene	GeneService.thawLite(Gene gene)
Gene	GeneServiceImpl.thawLite(Gene gene)
Gene	GeneService.thawLiter(Gene gene)
Gene	GeneServiceImpl.thawLiter(Gene gene)

Method parameters in ubic.gemma.persistence.service.genome.gene with type arguments of type Gene

Modifier and Type	Method	Description
Collection<Gene>	GeneService.thawLite(Collection<Gene> genes)
Collection<Gene>	GeneServiceImpl.thawLite(Collection<Gene> genes)

Uses of Gene in ubic.gemma.persistence.service.genome.sequenceAnalysis

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

Modifier and Type	Method	Description
Collection<AnnotationAssociation>	AnnotationAssociationDao.find(Gene gene)
Collection<AnnotationAssociation>	AnnotationAssociationDaoImpl.find(Gene gene)
Collection<AnnotationAssociation>	AnnotationAssociationService.find(Gene gene)
Collection<AnnotationAssociation>	AnnotationAssociationServiceImpl.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationDao.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationService.find(Gene gene)
Collection<BlatAssociation>	BlatAssociationServiceImpl.find(Gene gene)

Uses of Gene in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
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 Gene

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, Gene gene, boolean stricter)
static void	BusinessKey.attachCriteria(Criteria queryObject, Gene gene, String propertyName)	Restricts the query to the provided Gene.
static void	BusinessKey.checkKey(Gene gene)
static void	BusinessKey.checkValidKey(Gene gene)
static void	BusinessKey.createQueryObject(Criteria queryObject, Gene gene)
static Collection<CompositeSequence>	CommonQueries.getCompositeSequences(Gene gene, Session session)	Given a gene, get all the composite sequences that map to it.

Method parameters in ubic.gemma.persistence.util with type arguments of type Gene

Modifier and Type	Method	Description
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 Gene in ubic.gemma.rest.util.args

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

Modifier and Type	Method	Description
Gene	GeneArgService.getEntity(AbstractEntityArg<?,Gene,GeneService> entityArg)	Retrieve the entity represented by this argument.
Gene	GeneArgService.getEntityWithTaxon(GeneArg<?> entityArg, Taxon taxon)	Obtain a gene from a specific taxon.

Methods in ubic.gemma.rest.util.args that return types with arguments of type Gene

Modifier and Type	Method	Description
List<Gene>	GeneArgService.getEntitiesWithTaxon(GeneArg<?> genes, Taxon taxon)	Obtain genes from a specific taxon.
List<Gene>	GeneArgService.getEntitiesWithTaxon(GeneArrayArg genes, Taxon taxon)	Obtain genes from a specific taxon.

Method parameters in ubic.gemma.rest.util.args with type arguments of type Gene

Modifier and Type	Method	Description
Gene	GeneArgService.getEntity(AbstractEntityArg<?,Gene,GeneService> entityArg)	Retrieve the entity represented by this argument.

Uses of Gene in ubic.gemma.web.util

Methods in ubic.gemma.web.util with parameters of type Gene

Modifier and Type	Method	Description
int	GeneSymbolComparator.compare(Gene o1, Gene o2)