Package ubic.gemma.core.search

Interface SearchSource

All Known Implementing Classes:

CompassSearchSource, DatabaseSearchSource

public interface SearchSource

Search source that provides SearchResult from a search engine.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
Collection<SearchResult<ArrayDesign>>	searchArrayDesign(SearchSettings settings)
Collection<SearchResult<BibliographicReference>>	searchBibliographicReference(SearchSettings settings)
Collection<SearchResult<BioSequence>>	searchBioSequence(SearchSettings settings)
Collection<SearchResult<?>>	searchBioSequenceAndGene(SearchSettings settings, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated. use searchBioSequence(SearchSettings) (SearchSettings)} instead
Collection<SearchResult<CompositeSequence>>	searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<?>>	searchCompositeSequenceAndGene(SearchSettings settings)	Deprecated. use searchCompositeSequence(SearchSettings) instead
Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<Gene>>	searchGene(SearchSettings settings)
Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings)

Method Detail

searchArrayDesign

Collection<SearchResult<ArrayDesign>> searchArrayDesign(SearchSettings settings)
                                                 throws SearchException

Throws:

SearchException

searchBibliographicReference

Collection<SearchResult<BibliographicReference>> searchBibliographicReference(SearchSettings settings)
                                                                       throws SearchException

Throws:

SearchException

searchExperimentSet

Collection<SearchResult<ExpressionExperimentSet>> searchExperimentSet(SearchSettings settings)
                                                               throws SearchException

Throws:

SearchException

searchBioSequence

Collection<SearchResult<BioSequence>> searchBioSequence(SearchSettings settings)
                                                 throws SearchException

Throws:

SearchException

searchBioSequenceAndGene

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

Deprecated.

use searchBioSequence(SearchSettings) (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

Collection<SearchResult<CompositeSequence>> searchCompositeSequence(SearchSettings settings)
                                                             throws SearchException

Throws:

SearchException

searchCompositeSequenceAndGene

@Deprecated
Collection<SearchResult<?>> searchCompositeSequenceAndGene(SearchSettings settings)
                                                    throws SearchException

Deprecated.

use searchCompositeSequence(SearchSettings) 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

Collection<SearchResult<ExpressionExperiment>> searchExpressionExperiment(SearchSettings settings)
                                                                   throws SearchException

Throws:

SearchException

searchGene

Collection<SearchResult<Gene>> searchGene(SearchSettings settings)
                                   throws SearchException

Throws:

SearchException

searchGeneSet

Collection<SearchResult<GeneSet>> searchGeneSet(SearchSettings settings)
                                         throws SearchException

Throws:

SearchException