Package ubic.gemma.core.search

Class GeneSetSearchImpl

java.lang.Object

ubic.gemma.core.search.GeneSetSearchImpl

All Implemented Interfaces:

GeneSetSearch

@Component
public class GeneSetSearchImpl
extends Object
implements GeneSetSearch

Author:

paul

Constructor Summary

Constructors

Constructor	Description
GeneSetSearchImpl()

Method Summary

Modifier and Type	Method	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.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneSetSearchImpl

public GeneSetSearchImpl()

Method Detail

findByGene

public Collection<GeneSet> findByGene(Gene gene)

Specified by:

findByGene in interface GeneSetSearch

Parameters:

gene - gene

Returns:

gene sets

See Also:

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

findGeneSetValueObjectByGoId

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

Description copied from interface: GeneSetSearch

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

Specified by:

findGeneSetValueObjectByGoId in interface GeneSetSearch

Parameters:

goId - go id

taxonId - taxon id

Returns:

a GeneSet or null if nothing is found

findByGoId

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

Description copied from interface: GeneSetSearch

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

Specified by:

findByGoId in interface GeneSetSearch

Parameters:

goId - go id

taxon - taxon

Returns:

a GeneSet or null if nothing is found

findByGoTermName

public Collection<GeneSet> findByGoTermName(String goTermName,
                                            @Nullable
                                            Taxon taxon)
                                     throws SearchException

Description copied from interface: GeneSetSearch

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

Specified by:

findByGoTermName in interface GeneSetSearch

Parameters:

goTermName - go term name

taxon - taxon

Returns:

a collection with the hits

Throws:

SearchException

findByGoTermName

public Collection<GeneSet> findByGoTermName(String goTermName,
                                            @Nullable
                                            Taxon taxon,
                                            @Nullable
                                            Integer maxGoTermsProcessed,
                                            @Nullable
                                            Integer maxGeneSetSize)
                                     throws SearchException

Description copied from interface: GeneSetSearch

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

Specified by:

findByGoTermName in interface GeneSetSearch

Parameters:

goTermName - go term name

taxon - taxon

maxGoTermsProcessed - max go terms

maxGeneSetSize - max gene set size

Returns:

a collection with the hits

Throws:

SearchException

findByName

public Collection<GeneSet> findByName(String name)

Specified by:

findByName in interface GeneSetSearch

Parameters:

name - name

Returns:

gene sets

See Also:

GeneSetService.findByName(java.lang.String)

findByName

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

Specified by:

findByName in interface GeneSetSearch

Parameters:

name - name

taxon - taxon

Returns:

gene sets

findGeneSetsByName

public Collection<GeneSet> findGeneSetsByName(String query,
                                              Long taxonId)
                                       throws SearchException

Description copied from interface: GeneSetSearch

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

Specified by:

findGeneSetsByName in interface GeneSetSearch

Parameters:

query - string to match to a gene set.

taxonId - taxon id

Returns:

collection of GeneSet

Throws:

SearchException

findByPhenotypeName

public Collection<GeneSetValueObject> findByPhenotypeName(String phenotypeQuery,
                                                          Taxon taxon)
                                                   throws SearchException

Specified by:

findByPhenotypeName in interface GeneSetSearch

Throws:

SearchException