Package ubic.gemma.core.search
Interface GeneSetSearch
- All Known Implementing Classes:
GeneSetSearchImpl
public interface GeneSetSearch
- Author:
- paul
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Method Summary
Modifier and TypeMethodDescriptionfindByGene(Gene gene) findByGoId(String goId, Taxon taxon) Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.findByGoTermName(String goTermName, Taxon taxon) finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistentfindByGoTermName(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 persistentfindByName(String name) findByName(String name, Taxon taxon) 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 GeneSetValueObjectsfindGeneSetValueObjectByGoId(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 Details
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findByGene
- Parameters:
gene- gene- Returns:
- gene sets
- See Also:
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findGeneSetValueObjectByGoId
Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.- Parameters:
goId- go idtaxonId- taxon id- Returns:
- a GeneSet or null if nothing is found
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findByGoId
Finds gene sets by exact match to goTermId eg: GO:0000002 Note: the gene set returned is not persistent.- Parameters:
goId- go idtaxon- taxon- Returns:
- a GeneSet or null if nothing is found
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findByGoTermName
finds gene sets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent- Parameters:
goTermName- go term nametaxon- taxon- Returns:
- a collection with the hits
- Throws:
SearchException
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findByGoTermName
Collection<GeneSet> findByGoTermName(String goTermName, @Nullable Taxon taxon, @Nullable Integer maxGoTermsProcessed, @Nullable Integer maxGeneSetSize) throws SearchException finds genesets by go term name eg: "trans-hexaPrenylTransTransferase activity" Note: the gene sets returned are not persistent- 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
- Parameters:
name- name- Returns:
- gene sets
- See Also:
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findByName
- Parameters:
name- nametaxon- taxon- Returns:
- gene sets
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findGeneSetsByName
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:
SearchException
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