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:

• for related methods.

Constructor Summary

Constructors

Constructor	Description
AnnotationController()

Method Summary

Modifier and Type	Method	Description
Collection<ubic.gemma.model.common.description.CharacteristicValueObject>	findTerm(String query, Long taxonId)	Find terms for tagging, etc.
Collection<OntologyTerm>	getCategoryTerms()	Obtain all category terms that can be used as characteristic categories.
Collection<OntologyProperty>	getRelationTerms()	Obtain all relation terms that can be used as predicate.
void	reinitializeOntologyIndices()	AJAX Note that this completely scraps the indices, and runs asynchronously.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AnnotationController

public AnnotationController()

Method Details

getCategoryTerms

public Collection<OntologyTerm> getCategoryTerms()

Obtain all category terms that can be used as characteristic categories.

AJAX

getRelationTerms

public Collection<OntologyProperty> getRelationTerms()

Obtain all relation terms that can be used as predicate.

AJAX

findTerm

public Collection<ubic.gemma.model.common.description.CharacteristicValueObject> findTerm(String query,
 @Nullable
 Long taxonId)

Find terms for tagging, etc.

AJAX

Parameters:

query - the query string

taxonId - only used for genes, but generally this restriction is problematic for factorValues, which is an important use case, ignored if null.

reinitializeOntologyIndices

public void reinitializeOntologyIndices()

AJAX Note that this completely scraps the indices, and runs asynchronously.