Annotation (OMERO API)

java.lang.Object
- ome.model.annotations.Annotation

All Implemented Interfaces:

Serializable, IAnnotated, IMutable, IObject, Filterable

Direct Known Subclasses:

BasicAnnotation, ListAnnotation, MapAnnotation, TextAnnotation, TypeAnnotation
```
@Entity
 @ClassBridge(name="details",
             impl=DetailsFieldBridge.class,
             index=UN_TOKENIZED,
             store=NO)
public abstract class Annotation
extends Object
implements Serializable, IObject, IMutable, IAnnotated
```
These filter definitions are used by the security system to eliminate non-readable objects from queries. The regular user does not need to worry about them, as they will be injected directly into the SQL (not HQL)

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Annotation.Details

Nested Classes
Modifier and Type	Class and Description
`static class`	`Annotation.Details`

Field Summary

Fields
Modifier and Type	Field and Description
`protected Map<String,Object>`	`_dynamicFields`
`protected boolean`	`_loaded`
`protected Set<AnnotationAnnotationLink>`	`annotationLinks`
`static String`	`ANNOTATIONLINKS`
`static String`	`ANNOTATIONLINKSCOUNTPEROWNER`
`protected String`	`description`
`static String`	`DESCRIPTION`
`protected Details`	`details`
`static String`	`DETAILS`
`static String`	`EVENT_FILTER`
`static String`	`EVENT_FILTER_ANNOTATIONLINKS`
`static Set<String>`	`FIELDS`
`static String`	`GROUP_FILTER`
`static String`	`GROUP_FILTER_ANNOTATIONLINKS`
`protected Long`	`id`
`static String`	`ID`
`protected String`	`name`
`static String`	`NAME`
`protected String`	`ns`
`static String`	`NS`
`static String`	`OWNER_FILTER`
`static String`	`OWNER_FILTER_ANNOTATIONLINKS`
`static String`	`PERMS_FILTER`
`static String`	`PERMS_FILTER_ANNOTATIONLINKS`
`protected Integer`	`version`
`static String`	`VERSION`

Constructor Summary

Constructors
Modifier Constructor and Description

Annotation()

protected Annotation(Long id)

Annotation(Long id, boolean loaded)
Main constructor.

Constructors
Modifier	Constructor and Description
	`Annotation()`
`protected`	`Annotation(Long id)`
	`Annotation(Long id, boolean loaded)` Main constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`acceptFilter(Filter __filter)`
`void`	`addAnnotationAnnotationLink(AnnotationAnnotationLink target)` use instead of setAnnotationLinks .
`void`	`addAnnotationAnnotationLink(AnnotationAnnotationLink link, boolean bothSides)` Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks, allowing for recursion -- whether or not addAnnotationAnnotationLink will be called on the addition if it is loaded
`void`	`addAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink> targets)` use like addAnnotationAnnotationLink.
`void`	`clearAnnotationLinks()` clears the set.
`<E> List<E>`	`collectAnnotationLinks(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.annotations.AnnotationAnnotationLink while collecting the results.
`<E> List<E>`	`eachLinkedAnnotation(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
`protected void`	`errorIfUnloaded()`
`Set<String>`	`fields()` returns a Set of field names that belong to this class
`Set<AnnotationAnnotationLink>`	`findAnnotationAnnotationLink(Annotation target)` find all ome.model.annotations.AnnotationAnnotationLink which have the argument as their child.
`protected Set<AnnotationAnnotationLink>`	`getAnnotationLinks()` returns annotationLinks .
`Map<Long,Long>`	`getAnnotationLinksCountPerOwner()` If fetched, returns the count(*) of ome.model.annotations.AnnotationAnnotationLink that a user has.
`String`	`getDescription()` Simple field ome.model.annotations.Annotation.description (java.lang.String)
`Details`	`getDetails()` The details of this object correspond to low-level system information.
`GraphHolder`	`getGraphHolder()` retrieves the `GraphHolder` for this entity.
`Long`	`getId()` The DB unique identifier for this object.
`String`	`getName()` Simple field ome.model.annotations.Annotation.name (java.lang.String)
`String`	`getNs()` Simple field ome.model.annotations.Annotation.ns (java.lang.String)
`Integer`	`getVersion()` This version number is controlled by the database for optimisitic locking.
`boolean`	`isLoaded()` transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
`boolean`	`isValid()` calls the class-specific validator for this instance and returns the value from `Validation.isValid()`
`Iterator<AnnotationAnnotationLink>`	`iterateAnnotationLinks()` should be used rather than accessing the annotationLinks set directly.
`AnnotationAnnotationLink`	`linkAnnotation(Annotation addition)` Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks .
`Iterator<Annotation>`	`linkedAnnotationIterator()` provides an iterator over the parent values of the annotationLinks.
`List<Annotation>`	`linkedAnnotationList()` produces a `List`-copy of the underlying collection.
`void`	`putAt(String field, Object value)` stores a value in this instance.
`void`	`removeAnnotationAnnotationLink(AnnotationAnnotationLink target)` removes a single element from this set and makes the inverse call on ome.model.annotations.AnnotationAnnotationLink
`void`	`removeAnnotationAnnotationLink(AnnotationAnnotationLink link, boolean bothSides)` removes the given AnnotationAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkAnnotation again if loaded.
`void`	`removeAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink> targets)` use like removeAnnotationAnnotationLink
`Object`	`retrieve(String field)` retrieves a value from this instance.
`protected void`	`setAnnotationLinks(Set<AnnotationAnnotationLink> annotationLinks)` setter for annotationLinks should be avoided.
`protected void`	`setAnnotationLinksCountPerOwner(Map<Long,Long> map)`
`void`	`setDescription(String description)`
`protected void`	`setDetails(Details details)` Use the `Details.copy(ome.model.internal.Details)` or `Details.shallowCopy(ome.model.internal.Details)` methods to set the `Annotation.Details` instance instead.
`void`	`setId(Long id)` usually unneeded.
`void`	`setName(String name)`
`void`	`setNs(String ns)`
`void`	`setVersion(Integer version)` use with caution.
`int`	`sizeOfAnnotationLinks()` returns the size of annotationLinks.
`protected void`	`throwNullCollectionException(String propertyName)`
`String`	`toString()`
`void`	`unlinkAnnotation(Annotation removal)` unlinks all ome.model.annotations.Annotation instances from this instance.
`void`	`unload()` set the loaded field to false, and set all non-ID fields to null.
`Collection<AnnotationAnnotationLink>`	`unmodifiableAnnotationLinks()` Returns an unmodifiable collection-view
`Validation`	`validate()` calls the class-specific validator for this instance and returns the `Validation` object.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - OWNER_FILTER
```
public static final String OWNER_FILTER
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER
```
public static final String GROUP_FILTER
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER
```
public static final String EVENT_FILTER
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER
```
public static final String PERMS_FILTER
```
    See Also:
    
    Constant Field Values
  - ID
```
public static final String ID
```
    See Also:
    
    Constant Field Values
  - id
```
protected Long id
```
  - VERSION
```
public static final String VERSION
```
    See Also:
    
    Constant Field Values
  - version
```
protected Integer version
```
  - ns
```
protected String ns
```
  - name
```
protected String name
```
  - description
```
protected String description
```
  - annotationLinks
```
protected Set<AnnotationAnnotationLink> annotationLinks
```
  - OWNER_FILTER_ANNOTATIONLINKS
```
public static final String OWNER_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER_ANNOTATIONLINKS
```
public static final String GROUP_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER_ANNOTATIONLINKS
```
public static final String EVENT_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER_ANNOTATIONLINKS
```
public static final String PERMS_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - details
```
protected Details details
```
  - NS
```
public static final String NS
```
    See Also:
    
    Constant Field Values
  - NAME
```
public static final String NAME
```
    See Also:
    
    Constant Field Values
  - DESCRIPTION
```
public static final String DESCRIPTION
```
    See Also:
    
    Constant Field Values
  - ANNOTATIONLINKSCOUNTPEROWNER
```
public static final String ANNOTATIONLINKSCOUNTPEROWNER
```
    See Also:
    
    Constant Field Values
  - ANNOTATIONLINKS
```
public static final String ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - DETAILS
```
public static final String DETAILS
```
    See Also:
    
    Constant Field Values
  - FIELDS
```
public static final Set<String> FIELDS
```
  - _dynamicFields
```
protected Map<String,Object> _dynamicFields
```
  - _loaded
```
protected boolean _loaded
```
- Constructor Detail
  - Annotation
```
public Annotation()
```
  - Annotation
```
protected Annotation(Long id)
```
  - Annotation
```
public Annotation(Long id,
                  boolean loaded)
```
    Main constructor.
- Method Detail
  - getId
```
@DocumentId
public Long getId()
```
    The DB unique identifier for this object. You are not responsible for setting the id; however, it can be useful for creating "unloaded" versions of your objects. Each top-level entity contains an id field of type long. For all objects returned from the server, this value will be non-null, which doesn't necessarily hold for the other fields.
    
    Specified by:
    
    getId in interface IObject
    
    Returns:
    
    Long primary key. May be null.
  - setId
```
public void setId(Long id)
```
    Description copied from interface: IObject
    
    usually unneeded. Ids are managed by the backend.
    
    Specified by:
    
    setId in interface IObject
    
    Parameters:
    
    id - Long value for this id.
  - getVersion
```
public Integer getVersion()
```
    This version number is controlled by the database for optimisitic locking.
    
    Specified by:
    
    getVersion in interface IMutable
  - setVersion
```
public void setVersion(Integer version)
```
    Description copied from interface: IMutable
    
    use with caution. In general, the version should only be altered by the backend. In the best case, an exception will be thrown for a version not equal to the current DB value. In the worst (though rare) case, the new version could match the database, and override optimistic lock checks that are supposed to prevent data loss.
    
    Specified by:
    
    setVersion in interface IMutable
    
    Parameters:
    
    version - Value for this objects version.
  - getNs
```
@Field(index=TOKENIZED) @Field(index=TOKENIZED,name="combined_fields")
public String getNs()
```
    Simple field ome.model.annotations.Annotation.ns (java.lang.String)
  - setNs
```
public void setNs(String ns)
```
  - getName
```
@Field(index=TOKENIZED) @Field(index=TOKENIZED,name="combined_fields")
public String getName()
```
    Simple field ome.model.annotations.Annotation.name (java.lang.String)
  - setName
```
public void setName(String name)
```
  - getDescription
```
@Field(index=TOKENIZED) @Field(index=TOKENIZED,name="combined_fields")
public String getDescription()
```
    Simple field ome.model.annotations.Annotation.description (java.lang.String)
  - setDescription
```
public void setDescription(String description)
```
  - getAnnotationLinks
```
protected Set<AnnotationAnnotationLink> getAnnotationLinks()
```
    returns annotationLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.annotations.Annotation.annotationLinks (ome.model.annotations.AnnotationAnnotationLink)
  - setAnnotationLinks
```
protected void setAnnotationLinks(Set<AnnotationAnnotationLink> annotationLinks)
```
    setter for annotationLinks should be avoided. Does not fulfill normal semantics.
  - sizeOfAnnotationLinks
```
public int sizeOfAnnotationLinks()
```
    returns the size of annotationLinks. If less than zero, the Set was null.
    
    Specified by:
    
    sizeOfAnnotationLinks in interface IAnnotated
  - iterateAnnotationLinks
```
public Iterator<AnnotationAnnotationLink> iterateAnnotationLinks()
```
    should be used rather than accessing the annotationLinks set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfAnnotationLinks() is less than zero.
    
    Specified by:
    
    iterateAnnotationLinks in interface IAnnotated
  - unmodifiableAnnotationLinks
```
public Collection<AnnotationAnnotationLink> unmodifiableAnnotationLinks()
```
    Returns an unmodifiable collection-view
    
    Specified by:
    
    unmodifiableAnnotationLinks in interface IAnnotated
  - collectAnnotationLinks
```
public <E> List<E> collectAnnotationLinks(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.annotations.AnnotationAnnotationLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateAnnotationLinks() internally and so will return a value even if the underlying collection is null.
    
    Specified by:
    
    collectAnnotationLinks in interface IAnnotated
  - addAnnotationAnnotationLink
```
public void addAnnotationAnnotationLink(AnnotationAnnotationLink target)
```
    use instead of setAnnotationLinks . Makes the necessary call on ome.model.annotations.AnnotationAnnotationLink as well.
  - addAnnotationAnnotationLinkSet
```
public void addAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink> targets)
```
    use like addAnnotationAnnotationLink.
  - removeAnnotationAnnotationLink
```
public void removeAnnotationAnnotationLink(AnnotationAnnotationLink target)
```
    removes a single element from this set and makes the inverse call on ome.model.annotations.AnnotationAnnotationLink
  - removeAnnotationAnnotationLinkSet
```
public void removeAnnotationAnnotationLinkSet(Collection<AnnotationAnnotationLink> targets)
```
    use like removeAnnotationAnnotationLink
  - linkAnnotation
```
public AnnotationAnnotationLink linkAnnotation(Annotation addition)
```
    Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks . This entails changing our annotationLinks Set, creating a new ome.model.annotations.AnnotationAnnotationLink and calling linkAnnotation on the ome.model.annotations.Annotation.
    
    Specified by:
    
    linkAnnotation in interface IAnnotated
  - addAnnotationAnnotationLink
```
public void addAnnotationAnnotationLink(AnnotationAnnotationLink link,
                                        boolean bothSides)
```
    Adds a ome.model.annotations.AnnotationAnnotationLink to annotationLinks, allowing for recursion -- whether or not addAnnotationAnnotationLink will be called on the addition if it is loaded
  - linkedAnnotationIterator
```
public Iterator<Annotation> linkedAnnotationIterator()
```
    provides an iterator over the parent values of the annotationLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedAnnotationList() instead.
    
    Specified by:
    
    linkedAnnotationIterator in interface IAnnotated
  - findAnnotationAnnotationLink
```
public Set<AnnotationAnnotationLink> findAnnotationAnnotationLink(Annotation target)
```
    find all ome.model.annotations.AnnotationAnnotationLink which have the argument as their child.
  - linkedAnnotationList
```
public List<Annotation> linkedAnnotationList()
```
    produces a List-copy of the underlying collection. Unlike, linkedAnnotationIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.
    
    Specified by:
    
    linkedAnnotationList in interface IAnnotated
  - eachLinkedAnnotation
```
public <E> List<E> eachLinkedAnnotation(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results. If block == null, then the iterator values themselves are collected.
    
    Specified by:
    
    eachLinkedAnnotation in interface IAnnotated
  - unlinkAnnotation
```
public void unlinkAnnotation(Annotation removal)
```
    unlinks all ome.model.annotations.Annotation instances from this instance.
    
    Specified by:
    
    unlinkAnnotation in interface IAnnotated
  - removeAnnotationAnnotationLink
```
public void removeAnnotationAnnotationLink(AnnotationAnnotationLink link,
                                           boolean bothSides)
```
    removes the given AnnotationAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkAnnotation again if loaded.
  - clearAnnotationLinks
```
public void clearAnnotationLinks()
```
    clears the set.
    
    Specified by:
    
    clearAnnotationLinks in interface IAnnotated
  - setAnnotationLinksCountPerOwner
```
protected void setAnnotationLinksCountPerOwner(Map<Long,Long> map)
```
  - getAnnotationLinksCountPerOwner
```
public Map<Long,Long> getAnnotationLinksCountPerOwner()
```
    If fetched, returns the count(*) of ome.model.annotations.AnnotationAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.
  - getDetails
```
public Details getDetails()
```
    The details of this object correspond to low-level system information. Owner, permissions, Details is always guaranteed to be non-null, unless the user actively nulls it. Every entity also contains a Detail reference, which doesn't refer to a separate table but rather to a collection of fields collected into a Hibernate "component" which is embedded in the object. HQL queries which refer to the Details component cannot directly fetch the entity like this: select o from Object join fetch o.details but rather each field of the Details instance must be explicitly joined: select o from Object join fetch o.details.owner It should also be noted that not all types have all the fields which are present on Details. For example, select e from Experimenter e join fetch e.details.owner will fail. Experimenter has no owner, for obvious reasons. Note: subclasses of this class will return a subclasse of the Details type.
    
    Specified by:
    
    getDetails in interface IObject
  - setDetails
```
protected void setDetails(Details details)
```
    Use the Details.copy(ome.model.internal.Details) or Details.shallowCopy(ome.model.internal.Details) methods to set the Annotation.Details instance instead.
  - isValid
```
public boolean isValid()
```
    Description copied from interface: IObject
    
    calls the class-specific validator for this instance and returns the value from Validation.isValid()
    
    Specified by:
    
    isValid in interface IObject
  - validate
```
public Validation validate()
```
    Description copied from interface: IObject
    
    calls the class-specific validator for this instance and returns the Validation object.
    
    Specified by:
    
    validate in interface IObject
    
    Returns:
    
    Validation collecting parameter.
  - acceptFilter
```
public boolean acceptFilter(Filter __filter)
```
    Specified by:
    
    acceptFilter in interface Filterable
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - fields
```
public Set<String> fields()
```
    Description copied from interface: IObject
    
    returns a Set of field names that belong to this class
    
    Specified by:
    
    fields in interface IObject
  - retrieve
```
public Object retrieve(String field)
```
    Description copied from interface: IObject
    
    retrieves a value from this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be retrieved from a lazy-loaded map filled by calls to IObject.putAt(String, Object)
    
    Specified by:
    
    retrieve in interface IObject
  - putAt
```
public void putAt(String field,
                  Object value)
```
    Description copied from interface: IObject
    
    stores a value in this instance. Values for field which match a field of this instance will be delegated to the accessors. Otherwise, values will be stored in a lazy-loaded map.
    
    Specified by:
    
    putAt in interface IObject
    
    Parameters:
    
    field - Field name
    
    value - Any object to be stored.
  - isLoaded
```
public boolean isLoaded()
```
    Description copied from interface: IObject
    
    transient field (not stored in the DB) which specifies whether this object has been loaded from the DB or is only a wrapper around the ID.
    
    Specified by:
    
    isLoaded in interface IObject
  - errorIfUnloaded
```
protected void errorIfUnloaded()
```
  - unload
```
public void unload()
```
    Description copied from interface: IObject
    
    set the loaded field to false, and set all non-ID fields to null. Subsequent calls to all accessors other than getId/setId will throw an ApiUsageException
    
    Specified by:
    
    unload in interface IObject
  - getGraphHolder
```
public final GraphHolder getGraphHolder()
```
    Description copied from interface: IObject
    
    retrieves the GraphHolder for this entity. If the GraphHolder has not been actively set, a new one will be instatiated.
    
    Specified by:
    
    getGraphHolder in interface IObject
    
    Returns:
    
    Non-null GraphHolder
  - throwNullCollectionException
```
protected void throwNullCollectionException(String propertyName)
```

Class Annotation

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

OWNER_FILTER

GROUP_FILTER

EVENT_FILTER

PERMS_FILTER

ID

id

VERSION

version

ns

name

description

annotationLinks

OWNER_FILTER_ANNOTATIONLINKS

GROUP_FILTER_ANNOTATIONLINKS

EVENT_FILTER_ANNOTATIONLINKS

PERMS_FILTER_ANNOTATIONLINKS

details

NS

NAME

DESCRIPTION

ANNOTATIONLINKSCOUNTPEROWNER

ANNOTATIONLINKS

DETAILS

FIELDS

_dynamicFields

_loaded

Constructor Detail

Annotation

Annotation

Annotation

Method Detail

getId

setId

getVersion

setVersion

getNs

setNs

getName

setName

getDescription

setDescription

getAnnotationLinks

setAnnotationLinks

sizeOfAnnotationLinks

iterateAnnotationLinks

unmodifiableAnnotationLinks

collectAnnotationLinks

addAnnotationAnnotationLink

addAnnotationAnnotationLinkSet

removeAnnotationAnnotationLink

removeAnnotationAnnotationLinkSet

linkAnnotation

addAnnotationAnnotationLink

linkedAnnotationIterator

findAnnotationAnnotationLink

linkedAnnotationList

eachLinkedAnnotation

unlinkAnnotation

removeAnnotationAnnotationLink

clearAnnotationLinks

setAnnotationLinksCountPerOwner

getAnnotationLinksCountPerOwner

getDetails

setDetails

isValid

validate

acceptFilter

toString

fields

retrieve

putAt

isLoaded

errorIfUnloaded