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.

Sources are used in the order they are passed to the CompositeSearchSource(List) constructor.

This source checks if the SearchSource are accepted by each individual source with SearchSource.accepts(SearchSettings) and subsequently delegate the operation.

It also supports logging of the time spent by each source and the number of results found. This is done at the DEBUG level unless the value set by setWarningThresholdMills(int) or setFastWarningThresholdMillis(int) is exceeded in which case WARNING is used.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
CompositeSearchSource(List<SearchSource> sources)

Method Summary

Modifier and Type	Method	Description
boolean	accepts(SearchSettings settings)	Indicate if this source accepts the given search settings.
Collection<SearchResult<ArrayDesign>>	searchArrayDesign(SearchSettings settings, SearchContext context)
Collection<SearchResult<BibliographicReference>>	searchBibliographicReference(SearchSettings settings, SearchContext context)
Collection<SearchResult<BioSequence>>	searchBioSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<?>>	searchBioSequenceAndGene(SearchSettings settings, SearchContext context, Collection<SearchResult<Gene>> previousGeneSearchResults)	Deprecated.
Collection<SearchResult<BlacklistedEntity>>	searchBlacklistedEntities(SearchSettings settings, SearchContext context)
Collection<SearchResult<CompositeSequence>>	searchCompositeSequence(SearchSettings settings, SearchContext context)
Collection<SearchResult<?>>	searchCompositeSequenceAndGene(SearchSettings settings, SearchContext context)	Deprecated.
Collection<SearchResult<ExpressionExperimentSet>>	searchExperimentSet(SearchSettings settings, SearchContext context)
Collection<SearchResult<ExpressionExperiment>>	searchExpressionExperiment(SearchSettings settings, SearchContext context)
Collection<SearchResult<Gene>>	searchGene(SearchSettings settings, SearchContext context)
Collection<SearchResult<GeneSet>>	searchGeneSet(SearchSettings settings, SearchContext context)
void	setFastWarningThresholdMillis(int fastWarningThresholdMillis)	Threshold in milliseconds for a warning to be logged when searching with SearchSettings.SearchMode.FAST.
void	setWarningThresholdMills(int warningThresholdMills)	Threshold in milliseconds for a warning to be logged.

Methods inherited from class java.lang.Object

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

Constructor Details

CompositeSearchSource

public CompositeSearchSource(List<SearchSource> sources)

Method Details

setFastWarningThresholdMillis

public void setFastWarningThresholdMillis(int fastWarningThresholdMillis)

Threshold in milliseconds for a warning to be logged when searching with SearchSettings.SearchMode.FAST.

The default is 100 ms.

setWarningThresholdMills

public void setWarningThresholdMills(int warningThresholdMills)

Threshold in milliseconds for a warning to be logged.

The default is 1000 ms.

accepts

public boolean accepts(SearchSettings settings)

Description copied from interface: SearchSource

Indicate if this source accepts the given search settings.

Specified by:

accepts in interface SearchSource

searchArrayDesign

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

Specified by:

searchArrayDesign in interface SearchSource

Throws:

SearchException

searchBibliographicReference

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

Specified by:

searchBibliographicReference in interface SearchSource

Throws:

SearchException

searchExperimentSet

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

Specified by:

searchExperimentSet in interface SearchSource

Throws:

SearchException

searchBioSequence

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

Specified by:

searchBioSequence in interface SearchSource

Throws:

SearchException

searchBioSequenceAndGene

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

Specified by:

searchCompositeSequence in interface SearchSource

Throws:

SearchException

searchCompositeSequenceAndGene

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

Specified by:

searchExpressionExperiment in interface SearchSource

Throws:

SearchException

searchGene

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

Specified by:

searchGene in interface SearchSource

Throws:

SearchException

searchGeneSet

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

Specified by:

searchGeneSet in interface SearchSource

Throws:

SearchException

searchBlacklistedEntities

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

Specified by:

searchBlacklistedEntities in interface SearchSource

Throws:

SearchException