Uses of Class
ubic.gemma.model.common.search.SearchSettings

Packages that use SearchSettings

Package	Description
ubic.gemma.core.search
ubic.gemma.core.search.lucene
ubic.gemma.core.search.source
ubic.gemma.model.common.search
ubic.gemma.rest

Uses of SearchSettings in ubic.gemma.core.search

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

Modifier and Type	Method	Description
boolean	SearchSource.accepts(SearchSettings settings)	Indicate if this source accepts the given search settings.
static <T extends Identifiable> boolean	SearchSettingsUtils.isFilled(Collection<SearchResult<T>> results, SearchSettings settings)	Check if a collection of search results is already filled.
SearchService.SearchResultMap	SearchService.search(SearchSettings settings)
SearchService.SearchResultMap	SearchService.search(SearchSettings settings, SearchContext context)	The results are sorted in order of decreasing score, organized by class.
SearchService.SearchResultMap	SearchServiceImpl.search(SearchSettings settings)
SearchService.SearchResultMap	SearchServiceImpl.search(SearchSettings settings, SearchContext context)
default Collection<SearchResult<ArrayDesign>>	SearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)
default Collection<SearchResult<BibliographicReference>>	SearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)
default Collection<SearchResult<BioSequence>>	SearchSource.searchBioSequence(SearchSettings settings, SearchContext context)
default Collection<SearchResult<?>>	SearchSource.searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use SearchSource.searchBioSequence(SearchSettings, SearchContext) (SearchSettings)} instead
default Collection<SearchResult<BlacklistedEntity>>	SearchSource.searchBlacklistedEntities(SearchSettings settings, SearchContext context)
default Collection<SearchResult<CompositeSequence>>	SearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
default Collection<SearchResult<?>>	SearchSource.searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Deprecated. use SearchSource.searchCompositeSequence(SearchSettings, SearchContext) instead
default Collection<SearchResult<ExpressionExperimentSet>>	SearchSource.searchExperimentSet(SearchSettings settings, SearchContext context)
default Collection<SearchResult<ExpressionExperiment>>	SearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
default Collection<SearchResult<Gene>>	SearchSource.searchGene(SearchSettings settings, SearchContext context)
default Collection<SearchResult<GeneSet>>	SearchSource.searchGeneSet(SearchSettings settings, SearchContext context)

Constructors in ubic.gemma.core.search with parameters of type SearchSettings

Modifier	Constructor	Description
	SearchResultSet(SearchSettings settings)

Uses of SearchSettings in ubic.gemma.core.search.lucene

Methods in ubic.gemma.core.search.lucene with parameters of type SearchSettings

Modifier and Type	Method	Description
static Set<String>	LuceneQueryUtils.extractTerms(SearchSettings settings, Consumer<Throwable> issueReporter)	Extract terms, regardless of their logical organization.
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings, boolean allowWildcards, Consumer<Throwable> issueReporter)	Extract a DNF (Disjunctive Normal Form) from the terms of a query.
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings, Consumer<Throwable> issueReporter)
static boolean	LuceneQueryUtils.isWildcard(SearchSettings settings)	Check if the query is a wildcard query.
static org.apache.lucene.search.Query	LuceneQueryUtils.parseSafely(SearchSettings settings, org.apache.lucene.queryParser.QueryParser queryParser, Consumer<Throwable> issueReporter)	Safely parse the given search settings into a Lucene query, falling back on a query with special characters escaped if necessary.
static String	LuceneQueryUtils.prepareDatabaseQuery(SearchSettings settings, boolean allowWildcards, Consumer<Throwable> issueReporter)	Obtain a query suitable for a database match.
static String	LuceneQueryUtils.prepareDatabaseQuery(SearchSettings settings, Consumer<Throwable> issueReporter)	Escape the query for a database match.
static URI	LuceneQueryUtils.prepareTermUriQuery(SearchSettings settings, Consumer<Throwable> issueReporter)

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

Methods in ubic.gemma.core.search.source with parameters of type SearchSettings

Modifier and Type	Method	Description
boolean	CompositeSearchSource.accepts(SearchSettings settings)
boolean	DatabaseSearchSource.accepts(SearchSettings settings)
boolean	GeneOntologySearchSource.accepts(SearchSettings settings)
boolean	HibernateSearchSource.accepts(SearchSettings settings)
boolean	OntologySearchSource.accepts(SearchSettings settings)
Collection<SearchResult<ArrayDesign>>	CompositeSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)
Collection<SearchResult<ArrayDesign>>	DatabaseSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)	A general search for array designs.
Collection<SearchResult<ArrayDesign>>	HibernateSearchSource.searchArrayDesign(SearchSettings settings, SearchContext context)
Collection<SearchResult<BibliographicReference>>	CompositeSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)
Collection<SearchResult<BibliographicReference>>	HibernateSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)
Collection<SearchResult<BioSequence>>	CompositeSearchSource.searchBioSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<BioSequence>>	DatabaseSearchSource.searchBioSequence(SearchSettings settings, SearchContext context)	A database search for biosequences.
Collection<SearchResult<BioSequence>>	HibernateSearchSource.searchBioSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<?>>	CompositeSearchSource.searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated.
Collection<SearchResult<?>>	DatabaseSearchSource.searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)
Collection<SearchResult<BlacklistedEntity>>	CompositeSearchSource.searchBlacklistedEntities(SearchSettings settings, SearchContext context)
Collection<SearchResult<BlacklistedEntity>>	DatabaseSearchSource.searchBlacklistedEntities(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	CompositeSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	DatabaseSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	HibernateSearchSource.searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<?>>	CompositeSearchSource.searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Deprecated.
Collection<SearchResult<?>>	DatabaseSearchSource.searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Search the DB for composite sequences and the genes that are matched to them.
Collection<SearchResult<ExpressionExperimentSet>>	CompositeSearchSource.searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperimentSet>>	DatabaseSearchSource.searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperimentSet>>	HibernateSearchSource.searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	CompositeSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	DatabaseSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)	Does search on exact string by: id, name and short name.
Collection<SearchResult<ExpressionExperiment>>	HibernateSearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	OntologySearchSource.searchExpressionExperiment(SearchSettings settings, SearchContext context)	Search via characteristics i.e.
Collection<SearchResult<Gene>>	CompositeSearchSource.searchGene(SearchSettings settings, SearchContext context)
Collection<SearchResult<Gene>>	DatabaseSearchSource.searchGene(SearchSettings settings, SearchContext context)	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, SearchContext context)
Collection<SearchResult<Gene>>	HibernateSearchSource.searchGene(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	CompositeSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	DatabaseSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	HibernateSearchSource.searchGeneSet(SearchSettings settings, SearchContext context)

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

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

Modifier and Type	Method	Description
static SearchSettings	SearchSettings.arrayDesignSearch(String query)	Convenience method to get pre-configured settings.
static SearchSettings	SearchSettings.bibliographicReferenceSearch(String query)	Convenience method to get pre-configured settings.
SearchSettings	SearchSettings.SearchSettingsBuilder.build()
static SearchSettings	SearchSettings.compositeSequenceSearch(String query, ArrayDesign arrayDesign)	Convenience method to get pre-configured settings.
static SearchSettings	SearchSettings.expressionExperimentSearch(String query)	Convenience method to get pre-configured settings.
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.
SearchSettings	SearchSettings.withExperimentConstraint(ExpressionExperiment experimentConstraint)
SearchSettings	SearchSettings.withFillResults(boolean fillResults)	Indicate if result objects (i.e.
SearchSettings	SearchSettings.withMaxResults(int maxResults)	Limit for the number of results per result type.
SearchSettings	SearchSettings.withMode(SearchSettings.SearchMode mode)	Indicate the search mode to use.
SearchSettings	SearchSettings.withPlatformConstraint(ArrayDesign platformConstraint)
SearchSettings	SearchSettings.withQuery(String query)	Processed query for performing a search.
SearchSettings	SearchSettings.withResultTypes(Set<Class<? extends Identifiable>> resultTypes)	Entities to retrieve.
SearchSettings	SearchSettings.withTaxonConstraint(Taxon taxonConstraint)
SearchSettings	SearchSettings.withUseDatabase(boolean useDatabase)	Use the database for finding results.
SearchSettings	SearchSettings.withUseFullTextIndex(boolean useFullTextIndex)	Use the full-text index for finding results.
SearchSettings	SearchSettings.withUseGeneOntology(boolean useGeneOntology)	Include results from the Gene Ontology (GO).
SearchSettings	SearchSettings.withUseOntology(boolean useOntology)	Use the ontology and ontology inference for finding results.

Uses of SearchSettings in ubic.gemma.rest

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

Modifier	Constructor	Description
	SearchSettingsValueObject(SearchSettings searchSettings)