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
void	createBiomaterialTag(ubic.gemma.model.common.description.Characteristic vc, Long id)
void	createExperimentTag(ubic.gemma.model.common.description.Characteristic vc, Long id)	Ajax
Collection<ubic.gemma.model.common.description.CharacteristicValueObject>	findTerm(String givenQueryString, Long taxonId)	AJAX.
Collection<OntologyTerm>	getCategoryTerms()
Collection<OntologyProperty>	getRelationTerms()
void	reinitializeOntologyIndices()	AJAX Note that this completely scraps the indices, and runs asynchronously.
void	removeBiomaterialTag(ubic.gemma.model.common.description.Characteristic vc, Long id)
void	removeExperimentTag(Collection<Long> characterIds, Long eeId)

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotationController

public AnnotationController()

Method Detail

getCategoryTerms

public Collection<OntologyTerm> getCategoryTerms()

getRelationTerms

public Collection<OntologyProperty> getRelationTerms()

createBiomaterialTag

public void createBiomaterialTag(ubic.gemma.model.common.description.Characteristic vc,
                                 Long id)

createExperimentTag

public void createExperimentTag(ubic.gemma.model.common.description.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<ubic.gemma.model.common.description.CharacteristicValueObject> findTerm(String givenQueryString,
                                                                                          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(ubic.gemma.model.common.description.Characteristic vc,
                                 Long id)

removeExperimentTag

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