Package ubic.gemma.core.search

Interface SearchSource

All Known Subinterfaces:

FieldAwareSearchSource

All Known Implementing Classes:

CompositeSearchSource, DatabaseSearchSource, GeneOntologySearchSource, HibernateSearchSource, OntologySearchSource

public interface SearchSource

Search source that provides SearchResult from a search engine.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
boolean	accepts(SearchSettings settings)	Indicate if this source accepts the given search settings.
default Collection<SearchResult<ArrayDesign>>	searchArrayDesign(SearchSettings settings, SearchContext context)
default Collection<SearchResult<BibliographicReference>>	searchBibliographicReference(SearchSettings settings, SearchContext context)
default Collection<SearchResult<BioSequence>>	searchBioSequence(SearchSettings settings, SearchContext context)
default Collection<SearchResult<?>>	searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use searchBioSequence(SearchSettings, SearchContext) (SearchSettings)} instead
default Collection<SearchResult<BlacklistedEntity>>	searchBlacklistedEntities(SearchSettings settings, SearchContext context)
default Collection<SearchResult<CompositeSequence>>	searchCompositeSequence(SearchSettings settings, SearchContext context)
default Collection<SearchResult<?>>	searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Deprecated. use searchCompositeSequence(SearchSettings, SearchContext) instead
default Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings, SearchContext context)
default Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings, SearchContext context)
default Collection<SearchResult<Gene>>	searchGene(SearchSettings settings, SearchContext context)
default Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings, SearchContext context)

Method Details

accepts

boolean accepts(SearchSettings settings)

Indicate if this source accepts the given search settings.

searchArrayDesign

default Collection<SearchResult<ArrayDesign>> searchArrayDesign(SearchSettings settings,
 SearchContext context)
                                                         throws SearchException

Throws:

SearchException

searchBibliographicReference

default Collection<SearchResult<BibliographicReference>> searchBibliographicReference(SearchSettings settings,
 SearchContext context)
                                                                               throws SearchException

Throws:

SearchException

searchExperimentSet

default Collection<SearchResult<ExpressionExperimentSet>> searchExperimentSet(SearchSettings settings,
 SearchContext context)
                                                                       throws SearchException

Throws:

SearchException

searchBioSequence

default Collection<SearchResult<BioSequence>> searchBioSequence(SearchSettings settings,
 SearchContext context)
                                                         throws SearchException

Throws:

SearchException

searchBioSequenceAndGene

@Deprecated
default Collection<SearchResult<?>> searchBioSequenceAndGene(SearchSettings settings,
 SearchContext context,
 @Nullable
 Collection<SearchResult<Gene>> previousGeneSearchResults)
                                                      throws SearchException

Deprecated.

use searchBioSequence(SearchSettings, SearchContext) (SearchSettings)} instead

Search for biosequence and, unfortunately genes.

I wanted to remove this, but there's some logic with indirect gene hit penalty that we might want to keep around.

Returns:

a mixture of BioSequence and Gene matching the search settings.

Throws:

SearchException

searchCompositeSequence

default Collection<SearchResult<CompositeSequence>> searchCompositeSequence(SearchSettings settings,
 SearchContext context)
                                                                     throws SearchException

Throws:

SearchException

searchCompositeSequenceAndGene

@Deprecated
default Collection<SearchResult<?>> searchCompositeSequenceAndGene(SearchSettings settings,
 SearchContext context)
                                                            throws SearchException

Deprecated.

use searchCompositeSequence(SearchSettings, SearchContext) instead

Search for composite sequences and, unfortunately, genes.

FIXME: this should solely return CompositeSequence

Returns:

a mixture of Gene and CompositeSequence matching the search settings

Throws:

SearchException

searchExpressionExperiment

default Collection<SearchResult<ExpressionExperiment>> searchExpressionExperiment(SearchSettings settings,
 SearchContext context)
                                                                           throws SearchException

Throws:

SearchException

searchGene

default Collection<SearchResult<Gene>> searchGene(SearchSettings settings,
 SearchContext context)
                                           throws SearchException

Throws:

SearchException

searchGeneSet

default Collection<SearchResult<GeneSet>> searchGeneSet(SearchSettings settings,
 SearchContext context)
                                                 throws SearchException

Throws:

SearchException

searchBlacklistedEntities

default Collection<SearchResult<BlacklistedEntity>> searchBlacklistedEntities(SearchSettings settings,
 SearchContext context)
                                                                       throws SearchException

Throws:

SearchException