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

Packages that use Taxon

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
ubic.gemma.core.analysis.report
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.service
ubic.gemma.core.association.phenotype
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.simple.model
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util.biomart
ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers
ubic.gemma.core.search
ubic.gemma.model.analysis.expression
ubic.gemma.model.common.search
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis
ubic.gemma.persistence.service.analysis.expression.coexpression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.association.coexpression
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.taxon
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.expression.arrayDesign

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

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

Modifier and Type	Method	Description
Taxon	LinkAnalysis.getTaxon()

Methods in ubic.gemma.core.analysis.expression.coexpression.links with parameters of type Taxon

Modifier and Type	Method	Description
void	LinkAnalysisPersister.initializeLinksFromOldData(Taxon t)	Temporary method.
void	LinkAnalysisPersisterImpl.initializeLinksFromOldData(Taxon t)
LinkAnalysis	LinkAnalysisService.processVectors(Taxon t, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)	Used when the input is data vectors from another source, instead of from a DB-bound expressionExperiment.
LinkAnalysis	LinkAnalysisServiceImpl.processVectors(Taxon t, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)
void	LinkAnalysis.setTaxon(Taxon taxon)

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

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

Modifier and Type	Method	Description
Map<Taxon,Long>	WhatsNew.getEeCountPerTaxon()
Map<Taxon,Collection<Long>>	WhatsNew.getNewEEIdsPerTaxon()
Map<Taxon,Collection<Long>>	WhatsNew.getUpdatedEEIdsPerTaxon()

Method parameters in ubic.gemma.core.analysis.report with type arguments of type Taxon

Modifier and Type	Method	Description
void	WhatsNew.setEeCountPerTaxon(Map<Taxon,Long> eeCountPerTaxon)
void	WhatsNew.setNewEEIdsPerTaxon(Map<Taxon,Collection<Long>> eeCountPerTaxon)
void	WhatsNew.setUpdatedEEIdsPerTaxon(Map<Taxon,Collection<Long>> map)

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

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

Modifier and Type	Method	Description
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	Blat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
Collection<BlatResult>	Blat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)	Run a BLAT search using the gfClient.
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, boolean sensitive, Taxon taxon)
Map<BioSequence,Collection<BlatResult>>	ShellDelegatingBlat.blatQuery(Collection<BioSequence> sequences, Taxon taxon)
Collection<BlatResult>	ShellDelegatingBlat.blatQuery(BioSequence b, Taxon taxon, boolean sensitive)
static ExternalDatabase	ShellDelegatingBlat.getSearchedGenome(Taxon taxon)
Collection<BlatResult>	Blat.processPsl(InputStream inputStream, Taxon taxon)
Collection<BlatResult>	ShellDelegatingBlat.processPsl(InputStream inputStream, Taxon taxon)

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

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

Modifier and Type	Method	Description
void	GeneMultifunctionalityPopulationService.updateMultifunctionality(Taxon t)
void	GeneMultifunctionalityPopulationServiceImpl.updateMultifunctionality(Taxon t)

Uses of Taxon in ubic.gemma.core.association.phenotype

Methods in ubic.gemma.core.association.phenotype with parameters of type Taxon

Modifier and Type	Method	Description
Collection<GeneEvidenceValueObject>	PhenotypeAssociationManagerService.findCandidateGenes(Collection<String> phenotypesValuesUris, Taxon taxon)	Deprecated. Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypes
Collection<GeneEvidenceValueObject>	PhenotypeAssociationManagerServiceImpl.findCandidateGenes(Collection<String> phenotypeValueUris, Taxon taxon)	Deprecated.
Map<String,Collection<? extends GeneValueObject>>	PhenotypeAssociationManagerService.findCandidateGenesForEach(Set<String> phenotypeUris, Taxon taxon)	Deprecated.
Map<String,Collection<? extends GeneValueObject>>	PhenotypeAssociationManagerServiceImpl.findCandidateGenesForEach(Set<String> phenotypeUris, Taxon taxon)	Deprecated.

Uses of Taxon in ubic.gemma.core.goldenpath

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

Modifier and Type	Method	Description
Taxon	GoldenPath.getTaxon()

Constructors in ubic.gemma.core.goldenpath with parameters of type Taxon

Constructor	Description
GoldenPath(Taxon taxon)	Create a GoldenPath database for a given taxon.
GoldenPathQuery(Taxon taxon)
GoldenPathSequenceAnalysis(Taxon taxon)

Uses of Taxon in ubic.gemma.core.loader.association

Constructor parameters in ubic.gemma.core.loader.association with type arguments of type Taxon

Constructor	Description
NCBIGene2GOAssociationParser(Collection<Taxon> taxa)

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

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

Modifier and Type	Method	Description
Taxon	ArrayDesignSequenceAlignmentService.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)	If no taxon is supplied then infer it from array.
Taxon	ArrayDesignSequenceAlignmentServiceImpl.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)
Taxon	ArrayDesignSequenceProcessingService.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)
Taxon	ArrayDesignSequenceProcessingServiceImpl.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)	If taxon is null then it has not been provided on the command line, then deduce the taxon from the arrayDesign.

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

Modifier and Type	Method	Description
static Collection<BioSequence>	ArrayDesignSequenceAlignmentServiceImpl.getSequences(ArrayDesign ad, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)	Use this to add sequences to an existing Affymetrix design.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processAffymetrixDesign(ArrayDesign arrayDesign, InputStream probeSequenceFile, Taxon taxon)
void	ArrayDesignProbeMapperService.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)	Annotate an array design using a direct source file.
void	ArrayDesignProbeMapperServiceImpl.processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds)
Collection<BlatResult>	ArrayDesignSequenceAlignmentService.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BlatResult>	ArrayDesignSequenceAlignmentServiceImpl.processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)	Read from FASTA file when the sequence file lacks any way to link the sequences back to the probes.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force)	Intended for use with array designs that use sequences that are in genbank, but the accessions need to be assigned after the array is already in the system.
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingService.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)	The sequence file must provide an unambiguous way to associate the sequences with design elements on the array.
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, InputStream sequenceIdentifierFile, SequenceType sequenceType, Taxon taxon)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile, String[] databaseNames, String blastDbHome, Taxon taxon, boolean force, FastaCmd fc)
Collection<BioSequence>	ArrayDesignSequenceProcessingServiceImpl.processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceFile, SequenceType sequenceType, Taxon taxon)
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)
Taxon	ArrayDesignSequenceAlignmentService.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)	If no taxon is supplied then infer it from array.
Taxon	ArrayDesignSequenceAlignmentServiceImpl.validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)
Taxon	ArrayDesignSequenceProcessingService.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)
Taxon	ArrayDesignSequenceProcessingServiceImpl.validateTaxon(Taxon taxon, ArrayDesign arrayDesign)	If taxon is null then it has not been provided on the command line, then deduce the taxon from the arrayDesign.

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

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

Modifier and Type	Method	Description
Taxon	GeoConverter.getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa)
Taxon	GeoConverterImpl.getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa)	This method determines the primary taxon on the array: There are 4 main branches of logic.

Method parameters in ubic.gemma.core.loader.expression.geo with type arguments of type Taxon

Modifier and Type	Method	Description
Taxon	GeoConverter.getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa)
Taxon	GeoConverterImpl.getPrimaryArrayTaxon(Collection<Taxon> platformTaxa, Collection<String> probeTaxa)	This method determines the primary taxon on the array: There are 4 main branches of logic.

Uses of Taxon in ubic.gemma.core.loader.expression.simple.model

Methods in ubic.gemma.core.loader.expression.simple.model that return Taxon

Modifier and Type	Method	Description
Taxon	SimpleExpressionExperimentMetaData.getTaxon()

Methods in ubic.gemma.core.loader.expression.simple.model with parameters of type Taxon

Modifier and Type	Method	Description
void	SimpleExpressionExperimentMetaData.setTaxon(Taxon taxon)

Uses of Taxon in ubic.gemma.core.loader.genome

Methods in ubic.gemma.core.loader.genome that return Taxon

Modifier and Type	Method	Description
Taxon	BlatResultParser.getTaxon()

Methods in ubic.gemma.core.loader.genome with parameters of type Taxon

Modifier and Type	Method	Description
void	BlatResultParser.setTaxon(Taxon taxon)

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

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

Modifier and Type	Method	Description
Collection<Taxon>	NcbiGeneDomainObjectGenerator.getSupportedTaxaWithNCBIGenes()	Those taxa that are supported by GEMMA and have genes in NCBI.

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

Modifier and Type	Method	Description
void	NcbiGeneLoader.load(String geneInfoFile, String gene2AccFile, String geneHistoryFile, String geneEnsemblFile, Taxon t)
void	NcbiGeneLoader.load(Taxon t)

Method parameters in ubic.gemma.core.loader.genome.gene.ncbi with type arguments of type Taxon

Modifier and Type	Method	Description
void	NcbiGeneLoader.updateTaxaWithGenesUsable(Collection<Taxon> taxaGenesLoaded)	Method to update taxon to indicate that genes have been loaded for that taxon are are usable.

Constructor parameters in ubic.gemma.core.loader.genome.gene.ncbi with type arguments of type Taxon

Constructor	Description
NcbiGeneDomainObjectGenerator(Collection<Taxon> taxa)

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

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

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

Uses of Taxon in ubic.gemma.core.loader.genome.taxon

Methods in ubic.gemma.core.loader.genome.taxon that return Taxon

Modifier and Type	Method	Description
Taxon	TaxonParser.get(Integer key)
Taxon	TaxonParser.parseOneLine(String line)

Methods in ubic.gemma.core.loader.genome.taxon that return types with arguments of type Taxon

Modifier and Type	Method	Description
Collection<Taxon>	TaxonParser.getResults()

Methods in ubic.gemma.core.loader.genome.taxon with parameters of type Taxon

Modifier and Type	Method	Description
protected Integer	TaxonParser.getKey(Taxon newItem)
protected void	TaxonParser.put(Integer key, Taxon value)

Uses of Taxon in ubic.gemma.core.loader.util.biomart

Methods in ubic.gemma.core.loader.util.biomart that return types with arguments of type Taxon

Modifier and Type	Method	Description
Map<Taxon,File>	BiomartEnsemblNcbiFetcher.fetch(Collection<Taxon> taxa)	Main method that iterates through each taxon supplied and calls the fetch method for each taxon.

Methods in ubic.gemma.core.loader.util.biomart with parameters of type Taxon

Modifier and Type	Method	Description
String	BiomartEnsemblNcbiFetcher.getBiomartTaxonName(Taxon gemmaTaxon)	Biomart taxon names are formatted as the scientific name all lowercase with the genus name shortened to one letter and appended to species name E.g.
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.parseTaxonBiomartFile(Taxon taxon, File taxonBiomartFile)	Method calls the parse method to parse a biomart file.
void	BiomartEnsembleNcbiParser.setTaxon(Taxon taxon)

Method parameters in ubic.gemma.core.loader.util.biomart with type arguments of type Taxon

Modifier and Type	Method	Description
Map<Taxon,File>	BiomartEnsemblNcbiFetcher.fetch(Collection<Taxon> taxa)	Main method that iterates through each taxon supplied and calls the fetch method for each taxon.
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.generate(Collection<Taxon> validTaxa)	Main method to generate a map of biomartEnsembleNcbiIds, involves optional fetch from biomart if no file is provided then returns results of parse method.
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.generateRemote(Collection<Taxon> validTaxa)

Constructors in ubic.gemma.core.loader.util.biomart with parameters of type Taxon

Constructor	Description
BiomartEnsembleNcbiParser(Taxon taxon, String[] attributesInFile)	Class needs to be initialised with taxon and which attributes have been used in query for biomart and thus what columns are in this file.

Uses of Taxon in ubic.gemma.core.ontology

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

Modifier and Type	Method	Description
Collection<CharacteristicValueObject>	OntologyService.findTermsInexact(String givenQueryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)	Given a search string will first look through the characteristic database for any entries that have a match.
Collection<CharacteristicValueObject>	OntologyServiceImpl.findTermsInexact(String queryString, int maxResults, Taxon taxon, long timeout, TimeUnit timeUnit)

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

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

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)

Uses of Taxon in ubic.gemma.core.search

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

Modifier and Type	Method	Description
GeneSet	GeneSetSearch.findByGoId(String goId, Taxon taxon)	Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
GeneSet	GeneSetSearchImpl.findByGoId(String goId, Taxon taxon)
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon)	finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearch.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)	finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon)
Collection<GeneSet>	GeneSetSearchImpl.findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize)
Collection<GeneSet>	GeneSetSearch.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetSearchImpl.findByName(String name, Taxon taxon)
Collection<GeneSetValueObject>	GeneSetSearch.findByPhenotypeName(String phenotypeQuery, Taxon taxon)
Collection<GeneSetValueObject>	GeneSetSearchImpl.findByPhenotypeName(String phenotypeQuery, Taxon taxon)

Uses of Taxon in ubic.gemma.model.analysis.expression

Methods in ubic.gemma.model.analysis.expression that return Taxon

Modifier and Type	Method	Description
Taxon	ExpressionExperimentSet.getTaxon()

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

Modifier and Type	Method	Description
void	ExpressionExperimentSet.setTaxon(Taxon taxon)

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

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

Modifier and Type	Method	Description
Taxon	SearchSettingsValueObject.getTaxon()

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

Modifier and Type	Method	Description
static SearchSettings	SearchSettings.expressionExperimentSearch(String query, Taxon taxon)	Convenience method to get pre-configured settings.
static SearchSettings	SearchSettings.geneSearch(String query, Taxon taxon)	Convenience method to get pre-configured settings.
void	SearchSettingsValueObject.setTaxon(Taxon taxon)

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

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

Modifier and Type	Method	Description
Taxon	ArrayDesign.getPrimaryTaxon()

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

Modifier and Type	Method	Description
static ArrayDesign	ArrayDesign.Factory.newInstance(String shortName, Taxon taxon)
void	ArrayDesign.setPrimaryTaxon(Taxon primaryTaxon)

Uses of Taxon in ubic.gemma.model.expression.biomaterial

Methods in ubic.gemma.model.expression.biomaterial that return Taxon

Modifier and Type	Method	Description
Taxon	BioMaterial.getSourceTaxon()

Methods in ubic.gemma.model.expression.biomaterial with parameters of type Taxon

Modifier and Type	Method	Description
void	BioMaterial.setSourceTaxon(Taxon sourceTaxon)

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

Methods in ubic.gemma.model.expression.experiment that return Taxon

Modifier and Type	Method	Description
Taxon	ExpressionExperiment.getTaxon()	This is a denormalization to speed up queries.

Methods in ubic.gemma.model.expression.experiment with parameters of type Taxon

Modifier and Type	Method	Description
void	ExpressionExperiment.setTaxon(Taxon taxon)

Uses of Taxon in ubic.gemma.model.genome

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

Modifier and Type	Method	Description
Taxon	Chromosome.getTaxon()
Taxon	Gene.getTaxon()
static Taxon	Taxon.Factory.newInstance()
static Taxon	Taxon.Factory.newInstance(String commonName)
static Taxon	Taxon.Factory.newInstance(String scientificName, String commonName, Integer ncbiId, boolean isGenesUsable)

Methods in ubic.gemma.model.genome with parameters of type Taxon

Modifier and Type	Method	Description
static TaxonValueObject	TaxonValueObject.fromEntity(Taxon taxon)
void	Gene.setTaxon(Taxon taxon)

Constructors in ubic.gemma.model.genome with parameters of type Taxon

Constructor	Description
Chromosome(String name, ExternalDatabase assemblyDatabase, BioSequence sequence, Taxon taxon)
Chromosome(String name, Taxon taxon)
TaxonValueObject(Taxon taxon)

Uses of Taxon in ubic.gemma.model.genome.biosequence

Methods in ubic.gemma.model.genome.biosequence that return Taxon

Modifier and Type	Method	Description
Taxon	BioSequence.getTaxon()

Methods in ubic.gemma.model.genome.biosequence with parameters of type Taxon

Modifier and Type	Method	Description
static BioSequence	BioSequence.Factory.newInstance(String name, Taxon taxon)
static BioSequence	BioSequence.Factory.newInstance(Taxon taxon)
void	BioSequence.setTaxon(Taxon taxon)

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

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

Constructor	Description
DatabaseBackedGeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)	default constructor to satisfy java bean contract
GeneSetValueObject(GeneSet geneSet, Taxon taxon, Long size)
GeneValueObject(Long geneId, String geneSymbol, String geneOfficialName, Taxon taxon)

Uses of Taxon in ubic.gemma.persistence.persister

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

Modifier and Type	Method	Description
protected Taxon	GenomePersister.persistTaxon(Taxon taxon, AbstractPersister.Caches caches)

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

Modifier and Type	Method	Description
protected Taxon	GenomePersister.persistTaxon(Taxon taxon, AbstractPersister.Caches caches)

Uses of Taxon in ubic.gemma.persistence.service.analysis

Methods in ubic.gemma.persistence.service.analysis with parameters of type Taxon

Modifier and Type	Method	Description
Collection<T>	AnalysisDao.findByTaxon(Taxon taxon)
Collection<T>	AnalysisService.findByTaxon(Taxon taxon)
Collection<T>	SingleExperimentAnalysisDaoBase.findByTaxon(Taxon taxon)
Collection<Long>	AnalysisService.getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
Collection<Long>	SingleExperimentAnalysisService.getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only

Uses of Taxon in ubic.gemma.persistence.service.analysis.expression.coexpression

Methods in ubic.gemma.persistence.service.analysis.expression.coexpression with parameters of type Taxon

Modifier and Type	Method	Description
Collection<CoexpressionAnalysis>	CoexpressionAnalysisService.findByTaxon(Taxon taxon)
Collection<CoexpressionAnalysis>	CoexpressionAnalysisServiceImpl.findByTaxon(Taxon taxon)
Collection<Long>	CoexpressionAnalysisService.getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
Collection<Long>	CoexpressionAnalysisServiceImpl.getExperimentsWithAnalysis(Taxon taxon)

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

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

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.findByTaxon(Taxon taxon)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.findByTaxon(Taxon taxon)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDao.findByTaxon(Taxon taxon)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisDaoImpl.findByTaxon(Taxon taxon)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisService.findByTaxon(Taxon taxon)
Collection<GeneDifferentialExpressionMetaAnalysis>	GeneDiffExMetaAnalysisServiceImpl.findByTaxon(Taxon taxon)
Collection<Long>	DifferentialExpressionAnalysisDao.getExperimentsWithAnalysis(Taxon taxon)
Collection<Long>	DifferentialExpressionAnalysisServiceImpl.getExperimentsWithAnalysis(Taxon taxon)
Collection<Long>	GeneDiffExMetaAnalysisServiceImpl.getExperimentsWithAnalysis(Taxon taxon)

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

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

Modifier and Type	Method	Description
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 Taxon

Modifier and Type	Method	Description
Collection<Gene>	Gene2GOAssociationDao.findByGoTermUris(Collection<String> uris, Taxon taxon)
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)

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

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

Modifier and Type	Method	Description
void	CoexpressionDao.deleteLinks(Taxon taxon, BioAssaySet experiment)
void	CoexpressionDaoImpl.deleteLinks(Taxon t, BioAssaySet experiment)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Find coexpression links for the genes that are common to at least stringency of the given datasets.
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes, limited to the given data sets.
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findInterCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findInterCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionDao.getCoexpression(Taxon taxon, BioAssaySet experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionDaoImpl.getCoexpression(Taxon taxon, BioAssaySet experiment, boolean quick)
List<Object[]>	CoexpressionDaoImpl.getRawCoexpressionFromDbViaGenes(Collection<Long> geneIds, Taxon t, int stringency)
boolean	CoexpressionDao.hasLinks(Taxon taxon, BioAssaySet ee)
boolean	CoexpressionDaoImpl.hasLinks(Taxon taxon, BioAssaySet ee)
void	CoexpressionService.updateNodeDegrees(Taxon taxon)
void	CoexpressionServiceImpl.updateNodeDegrees(Taxon t)

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

Constructor	Description
LinkCreator(Taxon taxon)

Uses of Taxon in ubic.gemma.persistence.service.association.phenotype

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

Modifier and Type	Method	Description
Collection<GeneEvidenceValueObject>	PhenotypeAssociationDao.findGenesWithPhenotypes(Set<String> phenotypesValueUri, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Collection<GeneEvidenceValueObject>	PhenotypeAssociationDaoImpl.findGenesWithPhenotypes(Set<String> phenotypeUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)	Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases : 1- Admin - can see anything 2- user not logged in - only public data 3- user logged in only showing what he has read access - public, shared + owned 4- user logged in only showing what he has write access - owned.
Map<String,Set<Integer>>	PhenotypeAssociationDao.findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	PhenotypeAssociationDaoImpl.findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)	find all private phenotypes associated with genes on a specific taxon and containing the valuesUri
Map<String,Set<Integer>>	PhenotypeAssociationDao.findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	PhenotypeAssociationDaoImpl.findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)	find all public phenotypes associated with genes on a specific taxon and containing the valuesUri

Uses of Taxon in ubic.gemma.persistence.service.association.phenotype.service

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

Modifier and Type	Method	Description
Collection<GeneEvidenceValueObject>	PhenotypeAssociationService.findGenesWithPhenotypes(Set<String> phenotypesValueUri, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Collection<GeneEvidenceValueObject>	PhenotypeAssociationServiceImpl.findGenesWithPhenotypes(Set<String> phenotypesValueUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Map<String,Set<Integer>>	PhenotypeAssociationService.findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	PhenotypeAssociationServiceImpl.findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	PhenotypeAssociationService.findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	PhenotypeAssociationServiceImpl.findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)

Uses of Taxon in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description with parameters of type Taxon

Modifier and Type	Method	Description
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDao.findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	Similar to CharacteristicDao.findExperimentsByUris(Collection, Taxon, int, boolean), but returns proxies with instead of initializing all the EEs in bulk.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentReferencesByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	Since proxies are returned, they cannot be collected in a HashSet which would otherwise cause their initialization by accessing Object.hashCode().
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDao.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)	This search looks at direct annotations, factor values and biomaterials in that order.
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicDaoImpl.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicService.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)
Map<Class<? extends Identifiable>,Map<String,Set<ExpressionExperiment>>>	CharacteristicServiceImpl.findExperimentsByUris(Collection<String> uris, Taxon taxon, int limit, boolean loadEEs, boolean rankByLevel)

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

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

Modifier and Type	Method	Description
Taxon	ArrayDesignService.getTaxon(Long id)
Taxon	ArrayDesignServiceImpl.getTaxon(Long id)

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

Modifier and Type	Method	Description
Map<Taxon,Long>	ArrayDesignDao.getPerTaxonCount()
Map<Taxon,Long>	ArrayDesignDaoImpl.getPerTaxonCount()
Map<Taxon,Long>	ArrayDesignService.getPerTaxonCount()
Map<Taxon,Long>	ArrayDesignServiceImpl.getPerTaxonCount()
Collection<Taxon>	ArrayDesignDao.getTaxa(ArrayDesign arrayDesign)
Collection<Taxon>	ArrayDesignDaoImpl.getTaxa(ArrayDesign arrayDesign)
Collection<Taxon>	ArrayDesignService.getTaxa(ArrayDesign arrayDesign)	Return the taxa for the array design.
Collection<Taxon>	ArrayDesignServiceImpl.getTaxa(ArrayDesign arrayDesign)

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

Modifier and Type	Method	Description
Collection<ArrayDesign>	ArrayDesignDao.findByTaxon(Taxon taxon)
Collection<ArrayDesign>	ArrayDesignDaoImpl.findByTaxon(Taxon taxon)
Collection<ArrayDesign>	ArrayDesignService.findByTaxon(Taxon taxon)	Find by the primary taxon.
Collection<ArrayDesign>	ArrayDesignServiceImpl.findByTaxon(Taxon taxon)

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

Methods in ubic.gemma.persistence.service.expression.experiment that return Taxon

Modifier and Type	Method	Description
Taxon	ExpressionExperimentDao.getTaxon(BioAssaySet ee)	Determine the taxon for a given experiment or subset.
Taxon	ExpressionExperimentDaoImpl.getTaxon(BioAssaySet ee)
Taxon	ExpressionExperimentService.getTaxon(BioAssaySet bioAssaySet)	Returns the taxon of the given experiment or subset.
Taxon	ExpressionExperimentServiceImpl.getTaxon(BioAssaySet bioAssaySet)

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

Modifier and Type	Method	Description
Map<Taxon,Long>	ExpressionExperimentDao.getPerTaxonCount()	Obtain the count of distinct experiments per taxon.
Map<Taxon,Long>	ExpressionExperimentDao.getPerTaxonCount(Collection<Long> ids)	Obtain the count of distinct experiments per taxon for experiments with the given IDs.
Map<Taxon,Long>	ExpressionExperimentDaoImpl.getPerTaxonCount()
Map<Taxon,Long>	ExpressionExperimentDaoImpl.getPerTaxonCount(Collection<Long> ids)
Map<Taxon,Long>	ExpressionExperimentService.getPerTaxonCount()
Map<Taxon,Long>	ExpressionExperimentServiceImpl.getPerTaxonCount()
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentDao.getTaxa(Collection<T> bioAssaySets)
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentDaoImpl.getTaxa(Collection<T> bioAssaySets)
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentService.getTaxa(Collection<T> bioAssaySets)	Return the taxon for each of the given experiments (or subsets).
<T extends BioAssaySet> Map<T,Taxon>	ExpressionExperimentServiceImpl.getTaxa(Collection<T> bioAssaySets)
Map<Taxon,Long>	ExpressionExperimentService.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)	Calculate the usage frequency of taxa by the datasets matching the provided filters.
Map<Taxon,Long>	ExpressionExperimentServiceImpl.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)

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

Modifier and Type	Method	Description
Collection<Long>	ExpressionExperimentDao.filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<Long>	ExpressionExperimentDaoImpl.filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<Long>	ExpressionExperimentService.filterByTaxon(Collection<Long> ids, Taxon taxon)	Remove IDs of Experiments that are not from the given taxon.
Collection<Long>	ExpressionExperimentServiceImpl.filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByTaxon(Taxon taxon)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByTaxon(Taxon taxon)
ExpressionExperimentSet	ExpressionExperimentSetService.initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)
ExpressionExperimentSet	ExpressionExperimentSetServiceImpl.initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)	Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Special method for front-end access.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)

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

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

Modifier and Type	Method	Description
Collection<Chromosome>	ChromosomeDao.find(String name, Taxon taxon)
Collection<Chromosome>	ChromosomeDaoImpl.find(String name, Taxon taxon)
Collection<Chromosome>	ChromosomeService.find(String name, Taxon taxon)	Locate by name e.g.
Collection<Chromosome>	ChromosomeServiceImpl.find(String name, Taxon taxon)
Gene	GeneDao.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneDaoImpl.findByOfficialSymbol(String symbol, Taxon taxon)
Collection<Gene>	GeneDao.getMicroRnaByTaxon(Taxon taxon)
Collection<Gene>	GeneDaoImpl.getMicroRnaByTaxon(Taxon taxon)
Collection<Gene>	GeneDao.loadKnownGenes(Taxon taxon)
Collection<Gene>	GeneDaoImpl.loadKnownGenes(Taxon taxon)

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

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

Modifier and Type	Method	Description
Taxon	GeneSetDao.getTaxon(GeneSet geneSet)	Returns the taxon of an arbitrary member of the set.
Taxon	GeneSetDaoImpl.getTaxon(GeneSet geneSet)
Taxon	GeneSetService.getTaxon(GeneSet geneSet)	get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
Taxon	GeneSetServiceImpl.getTaxon(GeneSet geneSet)

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

Modifier and Type	Method	Description
List<Taxon>	GeneSetDao.getTaxa(GeneSet geneSet)	Return all the taxa of the gene set members.
List<Taxon>	GeneSetDaoImpl.getTaxa(GeneSet geneSet)
Set<Taxon>	GeneSetService.getTaxa(GeneSet geneSet)	Obtain all the taxa for the members of a given gene set.
Set<Taxon>	GeneSetServiceImpl.getTaxa(GeneSet geneSet)

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

Modifier and Type	Method	Description
Collection<GeneProduct>	GeneProductDao.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductDaoImpl.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductService.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductServiceImpl.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetDao.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetDaoImpl.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetService.findByName(String name, Taxon taxon)
Collection<GeneSet>	GeneSetServiceImpl.findByName(String name, Taxon taxon)
Gene	GeneService.findByOfficialSymbol(String symbol, Taxon taxon)
Gene	GeneServiceImpl.findByOfficialSymbol(String symbol, Taxon taxon)
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<GeneSet>	GeneSetDao.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetDaoImpl.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetService.loadAll(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadAll(Taxon tax)
Collection<Gene>	GeneService.loadMicroRNAs(Taxon taxon)
Collection<Gene>	GeneServiceImpl.loadMicroRNAs(Taxon taxon)
Collection<GeneSet>	GeneSetService.loadMyGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadMyGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetService.loadMySharedGeneSets(Taxon tax)
Collection<GeneSet>	GeneSetServiceImpl.loadMySharedGeneSets(Taxon tax)

Uses of Taxon in ubic.gemma.persistence.service.genome.taxon

Methods in ubic.gemma.persistence.service.genome.taxon that return Taxon

Modifier and Type	Method	Description
Taxon	TaxonDaoImpl.create(Taxon taxon)
Taxon	TaxonDaoImpl.find(Taxon taxon)
Taxon	TaxonDao.findByCommonName(String commonName)
Taxon	TaxonDaoImpl.findByCommonName(String commonName)
Taxon	TaxonService.findByCommonName(String commonName)
Taxon	TaxonServiceImpl.findByCommonName(String commonName)
Taxon	TaxonDao.findByNcbiId(Integer ncbiId)
Taxon	TaxonDaoImpl.findByNcbiId(Integer ncbiId)
Taxon	TaxonService.findByNcbiId(Integer ncbiId)
Taxon	TaxonServiceImpl.findByNcbiId(Integer ncbiId)
Taxon	TaxonDao.findByScientificName(String scientificName)	Searches for a taxon by its scientific name, case insensitive.
Taxon	TaxonDaoImpl.findByScientificName(String scientificName)
Taxon	TaxonService.findByScientificName(String scientificName)
Taxon	TaxonServiceImpl.findByScientificName(String scientificName)
Taxon	TaxonService.findOrCreate(Taxon taxon)

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

Modifier and Type	Method	Description
Collection<Taxon>	TaxonDao.findTaxonUsedInEvidence()
Collection<Taxon>	TaxonDaoImpl.findTaxonUsedInEvidence()
Collection<Taxon>	TaxonService.loadAllTaxaWithGenes()
Collection<Taxon>	TaxonServiceImpl.loadAllTaxaWithGenes()

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

Modifier and Type	Method	Description
Taxon	TaxonDaoImpl.create(Taxon taxon)
protected TaxonValueObject	TaxonDaoImpl.doLoadValueObject(Taxon entity)
Taxon	TaxonDaoImpl.find(Taxon taxon)
Taxon	TaxonService.findOrCreate(Taxon taxon)
protected void	TaxonDaoImpl.initializeCachedFilteringResult(Taxon cachedEntity)
static boolean	TaxonUtils.isHuman(Taxon tax)
static boolean	TaxonUtils.isMouse(Taxon tax)
static boolean	TaxonUtils.isRat(Taxon tax)
void	TaxonService.remove(Taxon taxon)
void	TaxonService.update(Taxon taxon)

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

Modifier and Type	Method	Description
void	TaxonService.remove(Collection<Taxon> entities)
void	TaxonService.update(Collection<Taxon> entities)

Uses of Taxon in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.addRestrictions(Criteria queryObject, Taxon taxon)
static void	BusinessKey.attachCriteria(Criteria queryObject, Taxon taxon, String propertyName)	Restricts query to the given Taxon.
static void	BusinessKey.checkValidKey(Taxon taxon)

Uses of Taxon in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type Taxon

Constructor	Description
TaxonWithUsageStatisticsValueObject(Taxon taxon, Long numberOfExpressionExperiments)

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

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

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.
Gene	GeneArgService.getEntityWithTaxon(GeneArg<?> entityArg, Taxon taxon)	Obtain a gene from a specific taxon.
List<GeneEvidenceValueObject>	GeneArgService.getGeneEvidence(GeneArg<?> arg, Taxon taxon)	Deprecated.
List<GeneOntologyTermValueObject>	GeneArgService.getGeneGoTermsInTaxon(GeneArg<?> geneArg, Taxon taxon)	Obtain GO terms for the gene in the given taxon.
List<PhysicalLocationValueObject>	GeneArgService.getGeneLocationInTaxon(GeneArg<?> arg, Taxon taxon)	Returns all known locations of the gene that this GeneArg represents.
Slice<CompositeSequenceValueObject>	GeneArgService.getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit)	Obtain probes for the gene in the given taxon across all platforms.
Slice<GeneValueObject>	GeneArgService.getGenesInTaxon(Taxon taxon, int offset, int limit)
List<GeneValueObject>	GeneArgService.getGenesInTaxon(GeneArrayArg arg, Taxon taxon)

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

Modifier and Type	Method	Description
protected Map<String,List<String>>	TaxonArgService.getArgsByPropertyName(AbstractEntityArrayArg<Taxon,TaxonService> entitiesArg)
<A> Filters	TaxonArgService.getFilters(AbstractEntityArg<A,Taxon,TaxonService> entityArg)

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

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

Modifier and Type	Method	Description
Taxon	ArrayDesignAddCommand.getTaxon()

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

Modifier and Type	Method	Description
void	ArrayDesignAddCommand.setTaxon(Taxon taxon)

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

Modifier and Type	Method	Description
void	ArrayDesignValueObjectExt.setAdditionalTaxa(Collection<Taxon> t)	Method to format taxon list for display.