Package ubic.gemma.web.controller.expression.experiment

Class AnnotationController

java.lang.Object
ubic.gemma.web.controller.expression.experiment.AnnotationController
@Controller public class AnnotationController extends Object
Controller for methods involving annotation of experiments (and potentially other things); delegates to OntologyService and the CharacteristicService. Edits to characteristics are handled by
Author:
paul
See Also:

  • Constructor Details

    • AnnotationController

      public AnnotationController()

  • Method Details

    • getCategoryTerms

      public Collection<OntologyTerm> getCategoryTerms()

    • getRelationTerms

      public Collection<OntologyProperty> getRelationTerms()

    • createBiomaterialTag

      public void createBiomaterialTag(Characteristic vc, Long id)

    • createExperimentTag

      public void createExperimentTag(Characteristic vc, Long id)
      Ajax
      Parameters:
      vc - . If the evidence code is null, it will be filled in with IC. A category and value must be provided.
      id - of the expression experiment

    • findTerm

      public Collection<CharacteristicValueObject> findTerm(String givenQueryString, @Nullable Long taxonId)
      AJAX. Find terms for tagging, etc.
      Parameters:
      givenQueryString - the query string
      taxonId - only used for genes, but generally this restriction is problematic for factorValues, which is an important use case.

    • reinitializeOntologyIndices

      public void reinitializeOntologyIndices()
      AJAX Note that this completely scraps the indices, and runs asynchronously.

    • removeBiomaterialTag

      public void removeBiomaterialTag(Characteristic vc, Long id)

    • removeExperimentTag

      public void removeExperimentTag(Collection<Long> characterIds, Long eeId)