Uses of Class
ubic.gemma.model.common.description.BibliographicReference

Packages that use BibliographicReference

Package	Description
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.analysis
ubic.gemma.model.common.description
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.taglib	This package contains custom JSP tag libraries used in the Gemma Web application.

Uses of BibliographicReference in ubic.gemma.core.loader.entrez.pubmed

Methods in ubic.gemma.core.loader.entrez.pubmed that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	ExpressionExperimentBibRefFinder.locatePrimaryReference(ExpressionExperiment ee)
BibliographicReference	PubMedSearch.retrieve(String pubMedId)	Retrieve a single PubMed record by ID.

Methods in ubic.gemma.core.loader.entrez.pubmed that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
static Collection<BibliographicReference>	PubMedXMLParser.parse(InputStream is)
Collection<BibliographicReference>	PubMedSearch.retrieve(Collection<String> pubmedIds)	Retrieve multiple PubMed records by ID.
Collection<BibliographicReference>	PubMedSearch.searchAndRetrieve(String searchQuery, int maxResults)	Search based on terms and retrieve the PubMed records.
Collection<BibliographicReference>	PubMedSearch.searchAndRetrieveByDoi(String doi)	Retrieve PubMed records by DOI.

Methods in ubic.gemma.core.loader.entrez.pubmed with parameters of type BibliographicReference

Modifier and Type	Method	Description
static void	PubMedXMLParser.extractPublisher(BibliographicReference bibRef, Node item)
static void	PubMedXMLParser.processContributionDate(Node item, BibliographicReference bibRef)

Uses of BibliographicReference in ubic.gemma.core.search

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

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

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

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

Modifier and Type	Method	Description
Collection<SearchResult<BibliographicReference>>	CompositeSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)
Collection<SearchResult<BibliographicReference>>	HibernateSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)

Uses of BibliographicReference in ubic.gemma.model.analysis

Methods in ubic.gemma.model.analysis that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	Investigation.getPrimaryPublication()

Methods in ubic.gemma.model.analysis that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	Investigation.getOtherRelevantPublications()

Methods in ubic.gemma.model.analysis with parameters of type BibliographicReference

Modifier and Type	Method	Description
void	Investigation.setPrimaryPublication(BibliographicReference primaryPublication)

Method parameters in ubic.gemma.model.analysis with type arguments of type BibliographicReference

Modifier and Type	Method	Description
void	Investigation.setOtherRelevantPublications(Set<BibliographicReference> otherRelevantPublications)

Uses of BibliographicReference in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return BibliographicReference

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

Methods in ubic.gemma.model.common.description with parameters of type BibliographicReference

Modifier and Type	Method	Description
static CitationValueObject	BibliographicReferenceValueObject.constructCitation(BibliographicReference bib)
static CitationValueObject	CitationValueObject.convert2CitationValueObject(BibliographicReference ref)

Method parameters in ubic.gemma.model.common.description with type arguments of type BibliographicReference

Modifier and Type	Method	Description
static Collection<CitationValueObject>	BibliographicReferenceValueObject.constructCitations(Collection<BibliographicReference> bibs)
static List<CitationValueObject>	CitationValueObject.convert2CitationValueObjects(Collection<BibliographicReference> refs)
static List<BibliographicReferenceValueObject>	BibliographicReferenceValueObject.convert2ValueObjects(Collection<BibliographicReference> refs)	does not set related experiments field

Constructors in ubic.gemma.model.common.description with parameters of type BibliographicReference

Modifier	Constructor	Description
	BibliographicReferenceValueObject(BibliographicReference ref)	does not set related experiments field

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

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

Modifier and Type	Method	Description
BibliographicReference	ExpressionExperiment.getPrimaryPublication()

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	ExpressionExperiment.getOtherRelevantPublications()

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

Methods in ubic.gemma.model.genome.gene that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	GeneSet.getLiteratureSources()

Method parameters in ubic.gemma.model.genome.gene with type arguments of type BibliographicReference

Modifier and Type	Method	Description
void	GeneSet.setLiteratureSources(Set<BibliographicReference> literatureSources)

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

Methods in ubic.gemma.persistence.service.common.description that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	BibliographicReferenceService.create(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.find(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.find(BibliographicReference bibliographicReference)	check to see if the object already exists
BibliographicReference	BibliographicReferenceDao.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceDao.findByExternalId(DatabaseEntry externalId)	Find by the external database id, such as for PubMed
BibliographicReference	BibliographicReferenceDaoImpl.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceDaoImpl.findByExternalId(DatabaseEntry externalId)
BibliographicReference	BibliographicReferenceService.findByExternalId(String id)	Get a reference by the unqualified external id.
BibliographicReference	BibliographicReferenceService.findByExternalId(String id, String databaseName)	Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
BibliographicReference	BibliographicReferenceService.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(String id)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceService.findOrCreate(BibliographicReference BibliographicReference)
BibliographicReference	BibliographicReferenceService.refresh(String pubMedId)
BibliographicReference	BibliographicReferenceServiceImpl.refresh(String pubMedId)
BibliographicReference	BibliographicReferenceService.save(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDao.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.thaw(BibliographicReference bibliographicReference)

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
List<BibliographicReference>	BibliographicReferenceDaoImpl.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceDaoImpl.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceService.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceService.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceServiceImpl.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceServiceImpl.browse(int start, int limit, String orderField, boolean descending)
Collection<BibliographicReference>	BibliographicReferenceService.create(Collection<BibliographicReference> entities)
LinkedHashMap<BibliographicReference,Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceDao.getRelatedExperiments(int offset, int limit)	Get a slice of the references that are linked to experiments.
LinkedHashMap<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)	Get the related experiments for the given references.
LinkedHashMap<BibliographicReference,Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceDaoImpl.getRelatedExperiments(int offset, int limit)
LinkedHashMap<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceService.getRelatedExperiments(int offset, int limit)	Return all the BibRefs that are linked to ExpressionExperiments.
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceServiceImpl.getRelatedExperiments(int offset, int limit)
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Collection<BibliographicReference>	BibliographicReferenceService.save(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceDao.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceDaoImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)

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

Modifier and Type	Method	Description
BibliographicReference	BibliographicReferenceService.create(BibliographicReference bibliographicReference)
protected BibliographicReferenceValueObject	BibliographicReferenceDaoImpl.doLoadValueObject(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDaoImpl.find(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.find(BibliographicReference bibliographicReference)	check to see if the object already exists
BibliographicReference	BibliographicReferenceService.findOrCreate(BibliographicReference BibliographicReference)
BibliographicReferenceValueObject	BibliographicReferenceServiceImpl.loadValueObject(BibliographicReference entity)
void	BibliographicReferenceService.remove(BibliographicReference BibliographicReference)
BibliographicReference	BibliographicReferenceService.save(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDao.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.thaw(BibliographicReference bibliographicReference)
void	BibliographicReferenceService.update(BibliographicReference entity)

Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type BibliographicReference

Modifier and Type	Method	Description
Collection<BibliographicReference>	BibliographicReferenceService.create(Collection<BibliographicReference> entities)
LinkedHashMap<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)	Get the related experiments for the given references.
LinkedHashMap<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference,Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
void	BibliographicReferenceService.remove(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceService.save(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceDao.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceDaoImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
void	BibliographicReferenceService.update(Collection<BibliographicReference> entities)

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

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

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBibliographicReference(BibliographicReference bibRef)

Uses of BibliographicReference in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(BibliographicReference bibliographicReference)
static void	Thaws.thawBibliographicReference(BibliographicReference br)

Uses of BibliographicReference in ubic.gemma.web.taglib

Methods in ubic.gemma.web.taglib with parameters of type BibliographicReference

Modifier and Type	Method	Description
void	BibliographicReferenceMetaTag.setCitation(BibliographicReference citation)
void	ShortBibliographicReferenceTag.setCitation(BibliographicReference citation)