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.auditAndSecurity
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)	The results are sorted in order of decreasing score, organized by class.
SearchService.SearchResultMap	SearchServiceImpl.search(SearchSettings settings)
default Collection<SearchResult<ArrayDesign>>	SearchSource.searchArrayDesign(SearchSettings settings)
default Collection<SearchResult<BibliographicReference>>	SearchSource.searchBibliographicReference(SearchSettings settings)
default Collection<SearchResult<BioSequence>>	SearchSource.searchBioSequence(SearchSettings settings)
default Collection<SearchResult<?>>	SearchSource.searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
default Collection<SearchResult<BlacklistedEntity>>	SearchSource.searchBlacklistedEntities(SearchSettings settings)
default Collection<SearchResult<CompositeSequence>>	SearchSource.searchCompositeSequence(SearchSettings settings)
default Collection<SearchResult<?>>	SearchSource.searchCompositeSequenceAndGene(SearchSettings settings)	Deprecated. use SearchSource.searchCompositeSequence(SearchSettings) instead
default Collection<SearchResult<ExpressionExperimentSet>>	SearchSource.searchExperimentSet(SearchSettings settings)
default Collection<SearchResult<ExpressionExperiment>>	SearchSource.searchExpressionExperiment(SearchSettings settings)
default Collection<SearchResult<Gene>>	SearchSource.searchGene(SearchSettings settings)
default Collection<SearchResult<GeneSet>>	SearchSource.searchGeneSet(SearchSettings settings)

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

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)	Extract terms, regardless of their logical organization.
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings)
static Set<Set<String>>	LuceneQueryUtils.extractTermsDnf(SearchSettings settings, boolean allowWildcards)	Extract a DNF (Disjunctive Normal Form) from the terms of a query.
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)	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)	Escape the query for a database match.
static String	LuceneQueryUtils.prepareDatabaseQuery(SearchSettings settings, boolean allowWildcards)	Obtain a query suitable for a database match.
static URI	LuceneQueryUtils.prepareTermUriQuery(SearchSettings settings)

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

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

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

Modifier and Type	Method	Description
SearchSettings	UserQuery.getSearchSettings()

Methods in ubic.gemma.model.common.auditAndSecurity with parameters of type SearchSettings

Modifier and Type	Method	Description
static UserQuery	UserQuery.Factory.newInstance(String url, String name, Date lastUsed, Integer autoRunFrequencyHours, SearchSettings searchSettings)
void	UserQuery.setSearchSettings(SearchSettings searchSettings)

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.
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.

Uses of SearchSettings in ubic.gemma.rest

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

Constructor	Description
SearchSettingsValueObject(SearchSettings searchSettings)