ubic.gemma.core.search

Interface GeneSetSearch

All Known Implementing Classes:

GeneSetSearchImpl

public interface GeneSetSearch

Author:

paul

Method Summary

Modifier and Type	Method and Description
Collection<GeneSet>	findByGene(Gene gene)
GeneSet	findByGoId(String goId, Taxon taxon) Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
Collection<GeneSet>	findByGoTermName(String goTermName, Taxon taxon) finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	findByGoTermName(String goTermName, Taxon taxon, Integer maxGoTermsProcessed, Integer maxGeneSetSize) finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent
Collection<GeneSet>	findByName(String name)
Collection<GeneSet>	findByName(String name, Taxon taxon)
Collection<GeneSetValueObject>	findByPhenotypeName(String phenotypeQuery, Taxon taxon)
Collection<GeneSet>	findGeneSetsByName(String query, Long taxonId) Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects
GOGroupValueObject	findGeneSetValueObjectByGoId(String goId, Long taxonId) Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.

Method Detail

findByGene

Collection<GeneSet> findByGene(Gene gene)

Parameters:

gene - gene

Returns:

gene sets

See Also:

GeneSetService.findByGene(ubic.gemma.model.genome.Gene)

findGeneSetValueObjectByGoId

@Nullable
GOGroupValueObject findGeneSetValueObjectByGoId(String goId,
                                                          @Nullable
                                                          Long taxonId)

Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.

Parameters:

goId - go id

taxonId - taxon id

Returns:

a GeneSet or null if nothing is found

findByGoId

@Nullable
GeneSet findByGoId(String goId,
                             @Nullable
                             Taxon taxon)

Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.

Parameters:

goId - go id

taxon - taxon

Returns:

a GeneSet or null if nothing is found

findByGoTermName

Collection<GeneSet> findByGoTermName(String goTermName,
                                     Taxon taxon)
                              throws ubic.basecode.ontology.search.OntologySearchException

finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent

Parameters:

goTermName - go term name

taxon - taxon

Returns:

a collection with the hits

Throws:

ubic.basecode.ontology.search.OntologySearchException

findByGoTermName

Collection<GeneSet> findByGoTermName(String goTermName,
                                     @Nullable
                                     Taxon taxon,
                                     @Nullable
                                     Integer maxGoTermsProcessed,
                                     @Nullable
                                     Integer maxGeneSetSize)
                              throws ubic.basecode.ontology.search.OntologySearchException

finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent

Parameters:

goTermName - go term name

taxon - taxon

maxGoTermsProcessed - max go terms

maxGeneSetSize - max gene set size

Returns:

a collection with the hits

Throws:

ubic.basecode.ontology.search.OntologySearchException

findByName

Collection<GeneSet> findByName(String name)

Parameters:

name - name

Returns:

gene sets

See Also:

GeneSetService.findByName(java.lang.String)

findByName

Collection<GeneSet> findByName(String name,
                               Taxon taxon)

Parameters:

name - name

taxon - taxon

Returns:

gene sets

findGeneSetsByName

Collection<GeneSet> findGeneSetsByName(String query,
                                       Long taxonId)
                                throws ubic.basecode.ontology.search.OntologySearchException

Similar to method of same name in GeneSetController.java but here: - no taxon needed - GO groups always searched - GeneSet objects returned instead of GeneSetValueObjects

Parameters:

query - string to match to a gene set.

taxonId - taxon id

Returns:

collection of GeneSet

Throws:

ubic.basecode.ontology.search.OntologySearchException

findByPhenotypeName

Collection<GeneSetValueObject> findByPhenotypeName(String phenotypeQuery,
                                                   Taxon taxon)
                                            throws ubic.basecode.ontology.search.OntologySearchException

Throws:

ubic.basecode.ontology.search.OntologySearchException