Package ubic.gemma.persistence.service.genome.gene

Interface GeneSearchService

All Known Implementing Classes:

GeneSearchServiceImpl

public interface GeneSearchService

Service for searching genes (and gene sets)

Author:

tvrossum

Method Summary

Modifier and Type	Method	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.

Method Detail

getGenesByGOId

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

Parameters:

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

taxonId - a taxan ID to retrieve results from, or null for genes in any taxon

Returns:

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

getGOGroupGenes

Collection<Gene> getGOGroupGenes(String goQuery,
                                 @Nullable
                                 Taxon taxon)
                          throws SearchException

Throws:

SearchException

searchGenesAndGeneGroups

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

Throws:

SearchException

searchMultipleGenes

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

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

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

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

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

Parameters:

query - gene names (symbols)

taxonId - taxon id

Returns:

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

Throws:

SearchException