AnnotationController (Gemma 1.31.4 API)

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`createBiomaterialTag(Characteristic vc, Long id)`
`void`	`createExperimentTag(Characteristic vc, Long id)`	Ajax
`Collection<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(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(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,
                                                      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)