Package ubic.gemma.web.controller.genome.gene

Class GenePickerController

java.lang.Object
ubic.gemma.web.controller.genome.gene.GenePickerController
@Controller public class GenePickerController extends Object
For 'live searches' from the web interface.
Author:
luke

  • Constructor Details

    • GenePickerController

      public GenePickerController()

  • Method Details

    • getGenes

      public Collection<ubic.gemma.model.genome.gene.GeneValueObject> getGenes(Collection<Long> geneIds)
      AJAX
      Parameters:
      geneIds - gene ids
      Returns:
      collection of gene entity objects; duplicates will be resolved.

    • getGenesByGOId

      public Collection<ubic.gemma.model.genome.gene.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

    • getGeneSetByGOId

      public ubic.gemma.model.genome.gene.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

    • getTaxa

      public Collection<ubic.gemma.model.genome.TaxonValueObject> getTaxa()
      AJAX
      Returns:
      a collection of the taxa in gemma (whether usable or not)

    • getTaxaWithArrays

      public Collection<ubic.gemma.model.genome.TaxonValueObject> getTaxaWithArrays()
      AJAX
      Returns:
      List of taxa with array designs in gemma

    • getTaxaWithDatasets

      public Collection<ubic.gemma.model.genome.TaxonValueObject> getTaxaWithDatasets()
      AJAX
      Returns:
      collection of taxa that have expression experiments available.

    • getTaxaWithGenes

      public Collection<ubic.gemma.model.genome.TaxonValueObject> getTaxaWithGenes()
      AJAX
      Returns:
      Taxon that have genes loaded into Gemma and that should be used

    • searchGenes

      public Collection<ubic.gemma.model.genome.gene.GeneValueObject> searchGenes(String query, Long taxonId)
      AJAX (used by GeneCombo.js)
      Parameters:
      query - query
      taxonId - taxon id
      Returns:
      Collection of Gene entity objects

    • searchGenesAndGeneGroups

      public Collection<ubic.gemma.core.search.SearchResultDisplayObject> searchGenesAndGeneGroups(String query, Long taxonId)
      AJAX (used by GeneAndGeneGroupCombo.js)
      Parameters:
      query - query
      taxonId - can be null
      Returns:
      Collection of SearchResultDisplayObject

    • searchGenesWithNCBIId

      public Collection<ubic.gemma.model.genome.gene.GeneValueObject> searchGenesWithNCBIId(String query, Long taxonId)
      AJAX (used by Phenocarta)
      Parameters:
      query - query
      taxonId - taxon id
      Returns:
      Collection of Gene entity objects

    • searchMultipleGenes

      public Collection<ubic.gemma.model.genome.gene.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

    • searchMultipleGenesGetMap

      public Map<String,ubic.gemma.model.genome.gene.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