Package ubic.gemma.core.search
Class GeneSetSearchImpl
- java.lang.Object
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- ubic.gemma.core.search.GeneSetSearchImpl
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- All Implemented Interfaces:
GeneSetSearch
@Component public class GeneSetSearchImpl extends Object implements GeneSetSearch
- Author:
- paul
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Constructor Summary
Constructors Constructor Description GeneSetSearchImpl()
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Method Summary
All Methods Instance Methods Concrete Methods 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 persistentCollection<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 persistentCollection<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 GeneSetValueObjectsGOGroupValueObject
findGeneSetValueObjectByGoId(String goId, Long taxonId)
Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.
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Method Detail
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findByGene
public Collection<GeneSet> findByGene(Gene gene)
- Specified by:
findByGene
in interfaceGeneSetSearch
- Parameters:
gene
- gene- Returns:
- gene sets
- See Also:
GeneSetService.findByGene(ubic.gemma.model.genome.Gene)
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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 interfaceGeneSetSearch
- Parameters:
goId
- go idtaxonId
- taxon id- Returns:
- a GeneSet or null if nothing is found
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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 interfaceGeneSetSearch
- Parameters:
goId
- go idtaxon
- taxon- Returns:
- a GeneSet or null if nothing is found
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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 interfaceGeneSetSearch
- Parameters:
goTermName
- go term nametaxon
- taxon- Returns:
- a collection with the hits
- Throws:
SearchException
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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 interfaceGeneSetSearch
- Parameters:
goTermName
- go term nametaxon
- taxonmaxGoTermsProcessed
- max go termsmaxGeneSetSize
- max gene set size- Returns:
- a collection with the hits
- Throws:
SearchException
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findByName
public Collection<GeneSet> findByName(String name)
- Specified by:
findByName
in interfaceGeneSetSearch
- Parameters:
name
- name- Returns:
- gene sets
- See Also:
GeneSetService.findByName(java.lang.String)
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findByName
public Collection<GeneSet> findByName(String name, Taxon taxon)
- Specified by:
findByName
in interfaceGeneSetSearch
- Parameters:
name
- nametaxon
- taxon- Returns:
- gene sets
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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 interfaceGeneSetSearch
- Parameters:
query
- string to match to a gene set.taxonId
- taxon id- Returns:
- collection of GeneSet
- Throws:
SearchException
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findByPhenotypeName
public Collection<GeneSetValueObject> findByPhenotypeName(String phenotypeQuery, Taxon taxon) throws SearchException
- Specified by:
findByPhenotypeName
in interfaceGeneSetSearch
- Throws:
SearchException
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