ubic.gemma.core.genome.gene.service

Class GeneSearchServiceImpl

java.lang.Object

ubic.gemma.core.genome.gene.service.GeneSearchServiceImpl

All Implemented Interfaces:

GeneSearchService

@Service
public class GeneSearchServiceImpl
extends Object
implements GeneSearchService

Service for searching genes (and gene sets)

Author:

tvrossum

Constructor Summary

Constructors

Constructor and Description
GeneSearchServiceImpl()
GeneSearchServiceImpl(SearchService searchService, gemma.gsec.SecurityService securityService, TaxonService taxonService, GeneSetSearch geneSetSearch, GeneSetService geneSetService, GeneService geneService, GeneOntologyService geneOntologyService, GeneSetValueObjectHelper geneSetValueObjectHelper)

Method Summary

Modifier and Type	Method and Description
Collection<GeneValueObject>	getGenesByGOId(String goId, Long taxonId) get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
Collection<Gene>	getGOGroupGenes(String goQuery, Taxon taxon)
Collection<SearchResultDisplayObject>	searchGenesAndGeneGroups(String query, Long taxonId)
Collection<GeneValueObject>	searchMultipleGenes(String query, Long taxonId) Search for multiple genes at once.
Map<String,GeneValueObject>	searchMultipleGenesGetMap(Collection<String> query, Long taxonId) Search for multiple genes at once.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneSearchServiceImpl

public GeneSearchServiceImpl()

GeneSearchServiceImpl

@Autowired
public GeneSearchServiceImpl(SearchService searchService,
                                        gemma.gsec.SecurityService securityService,
                                        TaxonService taxonService,
                                        GeneSetSearch geneSetSearch,
                                        GeneSetService geneSetService,
                                        GeneService geneService,
                                        GeneOntologyService geneOntologyService,
                                        GeneSetValueObjectHelper geneSetValueObjectHelper)

Method Detail

getGenesByGOId

public Collection<GeneValueObject> getGenesByGOId(String goId,
                                                  Long taxonId)

Description copied from interface: GeneSearchService

get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy

Specified by:

getGenesByGOId in interface GeneSearchService

Parameters:

goId - GO id that must be in the format "GO_#######"

taxonId - must not be null and must correspond to a taxon

Returns:

empty if goId was blank or taxonId didn't correspond to a taxon

getGOGroupGenes

public Collection<Gene> getGOGroupGenes(String goQuery,
                                        Taxon taxon)
                                 throws ubic.basecode.ontology.search.OntologySearchException

Specified by:

getGOGroupGenes in interface GeneSearchService

Throws:

ubic.basecode.ontology.search.OntologySearchException

searchGenesAndGeneGroups

public Collection<SearchResultDisplayObject> searchGenesAndGeneGroups(String query,
                                                                      Long taxonId)
                                                               throws SearchException

Specified by:

searchGenesAndGeneGroups in interface GeneSearchService

Throws:

SearchException

searchMultipleGenes

public Collection<GeneValueObject> searchMultipleGenes(String query,
                                                       Long taxonId)
                                                throws IOException,
                                                       SearchException

Description copied from interface: GeneSearchService

Search for multiple genes at once. This attempts to limit the number of genes per query to only one.

Specified by:

searchMultipleGenes in interface GeneSearchService

Parameters:

query - A list of gene names (symbols), one per line.

taxonId - taxon id

Returns:

collection of gene value objects

Throws:

IOException - when there are IO problems

SearchException

searchMultipleGenesGetMap

public Map<String,GeneValueObject> searchMultipleGenesGetMap(Collection<String> query,
                                                             Long taxonId)
                                                      throws SearchException

Description copied from interface: GeneSearchService

Search for multiple genes at once. This attempts to limit the number of genes per query to only one.

Specified by:

searchMultipleGenesGetMap in interface GeneSearchService

Parameters:

query - gene names (symbols)

taxonId - taxon id

Returns:

query with match. Null values means nothing was found for that key (query)

Throws:

SearchException