Class GenePickerController
- java.lang.Object
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- ubic.gemma.web.controller.genome.gene.GenePickerController
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@Controller public class GenePickerController extends Object
For 'live searches' from the web interface.- Author:
- luke
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Constructor Summary
Constructors Constructor Description GenePickerController()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Collection<GeneValueObject>
getGenes(Collection<Long> geneIds)
AJAXCollection<GeneValueObject>
getGenesByGOId(String goId, Long taxonId)
for AJAX get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchyGOGroupValueObject
getGeneSetByGOId(String goId, Long taxonId)
for AJAX get a gene set with all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchyCollection<TaxonValueObject>
getTaxa()
AJAXCollection<TaxonValueObject>
getTaxaWithArrays()
AJAXCollection<TaxonValueObject>
getTaxaWithDatasets()
AJAXCollection<TaxonValueObject>
getTaxaWithEvidence()
AJAXCollection<TaxonValueObject>
getTaxaWithGenes()
AJAXCollection<GeneValueObject>
searchGenes(String query, Long taxonId)
AJAX (used by GeneCombo.js)Collection<SearchResultDisplayObject>
searchGenesAndGeneGroups(String query, Long taxonId)
AJAX (used by GeneAndGeneGroupCombo.js)Collection<GeneValueObject>
searchGenesWithNCBIId(String query, Long taxonId)
AJAX (used by Phenocarta)Collection<GeneValueObject>
searchMultipleGenes(String query, Long taxonId)
AJAX Search for multiple genes at once.Map<String,GeneValueObject>
searchMultipleGenesGetMap(Collection<String> query, Long taxonId)
AJAX Search for multiple genes at once.
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Method Detail
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getGenes
public Collection<GeneValueObject> getGenes(Collection<Long> geneIds)
AJAX- Parameters:
geneIds
- gene ids- Returns:
- collection of gene entity objects; duplicates will be resolved.
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getGenesByGOId
public Collection<GeneValueObject> getGenesByGOId(String goId, Long taxonId)
for AJAX 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
- must not be null and must correspond to a taxon- Returns:
- Collection empty if goId was blank or taxonId didn't correspond to a taxon
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getGeneSetByGOId
public GOGroupValueObject getGeneSetByGOId(String goId, Long taxonId)
for AJAX get a gene set with 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
- must not be null and must correspond to a taxon- Returns:
- GOGroupValueObject empty if goId was blank or taxonId didn't correspond to a taxon
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getTaxa
public Collection<TaxonValueObject> getTaxa()
AJAX- Returns:
- a collection of the taxa in gemma (whether usable or not)
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getTaxaWithArrays
public Collection<TaxonValueObject> getTaxaWithArrays()
AJAX- Returns:
- List of taxa with array designs in gemma
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getTaxaWithDatasets
public Collection<TaxonValueObject> getTaxaWithDatasets()
AJAX- Returns:
- collection of taxa that have expression experiments available.
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getTaxaWithEvidence
public Collection<TaxonValueObject> getTaxaWithEvidence()
AJAX- Returns:
- Taxon that are on Phenocarta evidence
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getTaxaWithGenes
public Collection<TaxonValueObject> getTaxaWithGenes()
AJAX- Returns:
- Taxon that have genes loaded into Gemma and that should be used
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searchGenes
public Collection<GeneValueObject> searchGenes(String query, Long taxonId)
AJAX (used by GeneCombo.js)- Parameters:
query
- querytaxonId
- taxon id- Returns:
- Collection of Gene entity objects
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searchGenesAndGeneGroups
public Collection<SearchResultDisplayObject> searchGenesAndGeneGroups(String query, Long taxonId)
AJAX (used by GeneAndGeneGroupCombo.js)- Parameters:
query
- querytaxonId
- can be null- Returns:
- Collection of SearchResultDisplayObject
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searchGenesWithNCBIId
public Collection<GeneValueObject> searchGenesWithNCBIId(String query, Long taxonId)
AJAX (used by Phenocarta)- Parameters:
query
- querytaxonId
- taxon id- Returns:
- Collection of Gene entity objects
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searchMultipleGenes
public Collection<GeneValueObject> searchMultipleGenes(String query, Long taxonId) throws IOException
AJAX 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
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searchMultipleGenesGetMap
public Map<String,GeneValueObject> searchMultipleGenesGetMap(Collection<String> query, Long taxonId)
AJAX 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:
- map with each gene-query as a key and a collection of the search-results as the value
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