Package ubic.gemma.core.search.source

Class CompositeSearchSource

java.lang.Object

ubic.gemma.core.search.source.CompositeSearchSource

All Implemented Interfaces:

SearchSource

public class CompositeSearchSource
extends Object
implements SearchSource

A search source constituted of multiple other sources.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	CompositeSearchSource.SearchFunction<T extends Identifiable>

Constructor Summary

Constructors

Constructor	Description
CompositeSearchSource(List<SearchSource> sources)

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.
Collection<SearchResult<CompositeSequence>>	searchCompositeSequence(SearchSettings settings)
Collection<SearchResult<?>>	searchCompositeSequenceAndGene(SearchSettings settings)	Deprecated.
Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings)
Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings)
Collection<SearchResult<Gene>>	searchGene(SearchSettings settings)
Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CompositeSearchSource

public CompositeSearchSource(List<SearchSource> sources)

Method Detail

searchArrayDesign

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

Specified by:

searchArrayDesign in interface SearchSource

Throws:

SearchException

searchBibliographicReference

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

Specified by:

searchBibliographicReference in interface SearchSource

Throws:

SearchException

searchExperimentSet

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

Specified by:

searchExperimentSet in interface SearchSource

Throws:

SearchException

searchBioSequence

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

Specified by:

searchBioSequence in interface SearchSource

Throws:

SearchException

searchBioSequenceAndGene

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

Deprecated.

Description copied from interface: SearchSource

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.

Specified by:

searchBioSequenceAndGene in interface SearchSource

Returns:

a mixture of BioSequence and Gene matching the search settings.

Throws:

SearchException

searchCompositeSequence

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

Specified by:

searchCompositeSequence in interface SearchSource

Throws:

SearchException

searchCompositeSequenceAndGene

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

Deprecated.

Description copied from interface: SearchSource

Search for composite sequences and, unfortunately, genes.

FIXME: this should solely return CompositeSequence

Specified by:

searchCompositeSequenceAndGene in interface SearchSource

Returns:

a mixture of Gene and CompositeSequence matching the search settings

Throws:

SearchException

searchExpressionExperiment

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

Specified by:

searchExpressionExperiment in interface SearchSource

Throws:

SearchException

searchGene

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

Specified by:

searchGene in interface SearchSource

Throws:

SearchException

searchGeneSet

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

Specified by:

searchGeneSet in interface SearchSource

Throws:

SearchException