Roi (omero-model 5.5.1 API)

java.lang.Object
- ome.model.roi.Roi

All Implemented Interfaces:

java.io.Serializable, IAnnotated, IMutable, IObject, Filterable
```
@Entity
 @Indexed(index="FullText")
 @ClassBridge(name="details",
             impl=DetailsFieldBridge.class,
             index=UN_TOKENIZED,
             store=NO)
public class Roi
extends java.lang.Object
implements java.io.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 Roi.Details

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

Field Summary

Fields
Modifier and Type	Field and Description
`protected java.util.Map<java.lang.String,java.lang.Object>`	`_dynamicFields`
`protected boolean`	`_loaded`
`protected java.util.Set<RoiAnnotationLink>`	`annotationLinks`
`static java.lang.String`	`ANNOTATIONLINKS`
`static java.lang.String`	`ANNOTATIONLINKSCOUNTPEROWNER`
`protected java.lang.String`	`description`
`static java.lang.String`	`DESCRIPTION`
`protected Details`	`details`
`static java.lang.String`	`DETAILS`
`static java.lang.String`	`EVENT_FILTER`
`static java.lang.String`	`EVENT_FILTER_ANNOTATIONLINKS`
`static java.lang.String`	`EVENT_FILTER_FOLDERLINKS`
`static java.lang.String`	`EVENT_FILTER_SHAPES`
`static java.util.Set<java.lang.String>`	`FIELDS`
`protected java.util.Set<FolderRoiLink>`	`folderLinks`
`static java.lang.String`	`FOLDERLINKS`
`static java.lang.String`	`FOLDERLINKSCOUNTPEROWNER`
`static java.lang.String`	`GROUP_FILTER`
`static java.lang.String`	`GROUP_FILTER_ANNOTATIONLINKS`
`static java.lang.String`	`GROUP_FILTER_FOLDERLINKS`
`static java.lang.String`	`GROUP_FILTER_SHAPES`
`protected java.lang.Long`	`id`
`static java.lang.String`	`ID`
`protected Image`	`image`
`static java.lang.String`	`IMAGE`
`protected java.lang.String`	`name`
`static java.lang.String`	`NAME`
`static java.lang.String`	`OWNER_FILTER`
`static java.lang.String`	`OWNER_FILTER_ANNOTATIONLINKS`
`static java.lang.String`	`OWNER_FILTER_FOLDERLINKS`
`static java.lang.String`	`OWNER_FILTER_SHAPES`
`static java.lang.String`	`PERMS_FILTER`
`static java.lang.String`	`PERMS_FILTER_ANNOTATIONLINKS`
`static java.lang.String`	`PERMS_FILTER_FOLDERLINKS`
`static java.lang.String`	`PERMS_FILTER_SHAPES`
`protected java.util.List<Shape>`	`shapes`
`static java.lang.String`	`SHAPES`
`protected OriginalFile`	`source`
`static java.lang.String`	`SOURCE`
`protected java.lang.Integer`	`version`
`static java.lang.String`	`VERSION`

Constructor Summary

Constructors
Modifier Constructor and Description

Roi()

protected Roi(java.lang.Long id)

Roi(java.lang.Long id, boolean loaded)
Main constructor.

Constructors
Modifier	Constructor and Description
	`Roi()`
`protected`	`Roi(java.lang.Long id)`
	`Roi(java.lang.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`	`addFolderRoiLink(FolderRoiLink target)` use instead of setFolderLinks .
`void`	`addFolderRoiLink(FolderRoiLink link, boolean bothSides)` Adds a ome.model.containers.FolderRoiLink to folderLinks, allowing for recursion -- whether or not addFolderRoiLink will be called on the addition if it is loaded
`void`	`addFolderRoiLinkSet(java.util.Collection<FolderRoiLink> targets)` use like addFolderRoiLink.
`void`	`addRoiAnnotationLink(RoiAnnotationLink target)` use instead of setAnnotationLinks .
`void`	`addRoiAnnotationLink(RoiAnnotationLink link, boolean bothSides)` Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks, allowing for recursion -- whether or not addRoiAnnotationLink will be called on the addition if it is loaded
`void`	`addRoiAnnotationLinkSet(java.util.Collection<RoiAnnotationLink> targets)` use like addRoiAnnotationLink.
`void`	`addShape(Shape target)` use instead of setShapes .
`void`	`addShapeSet(java.util.Collection<Shape> targets)` use like addShape.
`void`	`clearAnnotationLinks()` clears the set.
`void`	`clearFolderLinks()` clears the set.
`void`	`clearShapes()` clears the set.
`<E> java.util.List<E>`	`collectAnnotationLinks(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.annotations.RoiAnnotationLink while collecting the results.
`<E> java.util.List<E>`	`collectFolderLinks(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.containers.FolderRoiLink while collecting the results.
`<E> java.util.List<E>`	`collectShapes(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.roi.Shape while collecting the results.
`<E> java.util.List<E>`	`eachLinkedAnnotation(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.annotations.Annotation while collecting the results.
`<E> java.util.List<E>`	`eachLinkedFolder(CBlock<E> block)` takes a CBlock and calls the block once for each ome.model.containers.Folder while collecting the results.
`protected void`	`errorIfUnloaded()`
`java.util.Set<java.lang.String>`	`fields()` returns a Set of field names that belong to this class
`java.util.Set<FolderRoiLink>`	`findFolderRoiLink(Folder target)` find all ome.model.containers.FolderRoiLink which have the argument as their parent.
`java.util.Set<RoiAnnotationLink>`	`findRoiAnnotationLink(Annotation target)` find all ome.model.annotations.RoiAnnotationLink which have the argument as their child.
`protected java.util.Set<RoiAnnotationLink>`	`getAnnotationLinks()` returns annotationLinks .
`java.util.Map<java.lang.Long,java.lang.Long>`	`getAnnotationLinksCountPerOwner()` If fetched, returns the count(*) of ome.model.annotations.RoiAnnotationLink that a user has.
`java.lang.String`	`getDescription()` Simple field ome.model.roi.Roi.description (java.lang.String)
`Details`	`getDetails()` The details of this object correspond to low-level system information.
`protected java.util.Set<FolderRoiLink>`	`getFolderLinks()` returns folderLinks .
`java.util.Map<java.lang.Long,java.lang.Long>`	`getFolderLinksCountPerOwner()` If fetched, returns the count(*) of ome.model.containers.FolderRoiLink that a user has.
`GraphHolder`	`getGraphHolder()` retrieves the `GraphHolder` for this entity.
`java.lang.Long`	`getId()` The DB unique identifier for this object.
`Image`	`getImage()` Many-to-one field ome.model.roi.Roi.image (ome.model.core.Image)
`java.lang.String`	`getName()` Simple field ome.model.roi.Roi.name (java.lang.String)
`Shape`	`getPrimaryShape()` Gets the first element of shapes which can be interpreted as the primary or default element in some situations.
`Shape`	`getShape(int index)` Gets the ome.model.roi.Shape at the given index.
`protected java.util.List<Shape>`	`getShapes()` returns shapes .
`OriginalFile`	`getSource()` Many-to-one field ome.model.roi.Roi.source (ome.model.core.OriginalFile)
`java.lang.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()`
`java.util.Iterator<RoiAnnotationLink>`	`iterateAnnotationLinks()` should be used rather than accessing the annotationLinks set directly.
`java.util.Iterator<FolderRoiLink>`	`iterateFolderLinks()` should be used rather than accessing the folderLinks set directly.
`java.util.Iterator<Shape>`	`iterateShapes()` should be used rather than accessing the shapes set directly.
`RoiAnnotationLink`	`linkAnnotation(Annotation addition)` Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks .
`java.util.Iterator<Annotation>`	`linkedAnnotationIterator()` provides an iterator over the parent values of the annotationLinks.
`java.util.List<Annotation>`	`linkedAnnotationList()` produces a `List`-copy of the underlying collection.
`java.util.Iterator<Folder>`	`linkedFolderIterator()` provides an iterator over the child values of the folderLinks.
`java.util.List<Folder>`	`linkedFolderList()` produces a `List`-copy of the underlying collection.
`FolderRoiLink`	`linkFolder(Folder addition)` Adds a ome.model.containers.FolderRoiLink to folderLinks .
`Roi`	`newInstance()`
`Roi`	`proxy()`
`void`	`putAt(java.lang.String field, java.lang.Object value)` stores a value in this instance.
`void`	`removeFolderRoiLink(FolderRoiLink target)` removes a single element from this set and makes the inverse call on ome.model.containers.FolderRoiLink
`void`	`removeFolderRoiLink(FolderRoiLink link, boolean bothSides)` removes the given FolderRoiLink from folderLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.
`void`	`removeFolderRoiLinkSet(java.util.Collection<FolderRoiLink> targets)` use like removeFolderRoiLink
`void`	`removeRoiAnnotationLink(RoiAnnotationLink target)` removes a single element from this set and makes the inverse call on ome.model.annotations.RoiAnnotationLink
`void`	`removeRoiAnnotationLink(RoiAnnotationLink link, boolean bothSides)` removes the given RoiAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.
`void`	`removeRoiAnnotationLinkSet(java.util.Collection<RoiAnnotationLink> targets)` use like removeRoiAnnotationLink
`void`	`removeShape(Shape target)` removes a single element from this set and makes the inverse call on ome.model.roi.Shape
`void`	`removeShapeSet(java.util.Collection<Shape> targets)` use like removeShape
`java.lang.Object`	`retrieve(java.lang.String field)` retrieves a value from this instance.
`protected void`	`setAnnotationLinks(java.util.Set<RoiAnnotationLink> annotationLinks)` setter for annotationLinks should be avoided.
`protected void`	`setAnnotationLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)`
`void`	`setDescription(java.lang.String description)`
`protected void`	`setDetails(Details details)`
`protected void`	`setFolderLinks(java.util.Set<FolderRoiLink> folderLinks)` setter for folderLinks should be avoided.
`protected void`	`setFolderLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)`
`void`	`setId(java.lang.Long id)` usually unneeded.
`void`	`setImage(Image image)`
`void`	`setName(java.lang.String name)`
`Shape`	`setPrimaryShape(Shape element)` Swaps the first element of shapes with the first instance of the given element.
`Shape`	`setShape(int index, Shape element)` Sets the ome.model.roi.Shape at the given index.
`protected void`	`setShapes(java.util.List<Shape> shapes)` setter for shapes should be avoided.
`void`	`setSource(OriginalFile source)`
`void`	`setVersion(java.lang.Integer version)` use with caution.
`int`	`sizeOfAnnotationLinks()` returns the size of annotationLinks.
`int`	`sizeOfFolderLinks()` returns the size of folderLinks.
`int`	`sizeOfShapes()` returns the size of shapes.
`protected void`	`throwNullCollectionException(java.lang.String propertyName)`
`java.lang.String`	`toString()`
`void`	`unlinkAnnotation(Annotation removal)` unlinks all ome.model.annotations.Annotation instances from this instance.
`void`	`unlinkFolder(Folder removal)` unlinks all ome.model.containers.Folder instances from this instance.
`void`	`unload()` set the loaded field to false, and set all non-ID fields to null.
`java.util.Collection<RoiAnnotationLink>`	`unmodifiableAnnotationLinks()` Returns an unmodifiable collection-view
`java.util.Collection<FolderRoiLink>`	`unmodifiableFolderLinks()` Returns an unmodifiable collection-view
`java.util.Collection<Shape>`	`unmodifiableShapes()` 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 java.lang.String OWNER_FILTER
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER
```
public static final java.lang.String GROUP_FILTER
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER
```
public static final java.lang.String EVENT_FILTER
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER
```
public static final java.lang.String PERMS_FILTER
```
    See Also:
    
    Constant Field Values
  - ID
```
public static final java.lang.String ID
```
    See Also:
    
    Constant Field Values
  - id
```
protected java.lang.Long id
```
  - VERSION
```
public static final java.lang.String VERSION
```
    See Also:
    
    Constant Field Values
  - version
```
protected java.lang.Integer version
```
  - name
```
protected java.lang.String name
```
  - shapes
```
protected java.util.List<Shape> shapes
```
  - OWNER_FILTER_SHAPES
```
public static final java.lang.String OWNER_FILTER_SHAPES
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER_SHAPES
```
public static final java.lang.String GROUP_FILTER_SHAPES
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER_SHAPES
```
public static final java.lang.String EVENT_FILTER_SHAPES
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER_SHAPES
```
public static final java.lang.String PERMS_FILTER_SHAPES
```
    See Also:
    
    Constant Field Values
  - image
```
protected Image image
```
  - source
```
protected OriginalFile source
```
  - folderLinks
```
protected java.util.Set<FolderRoiLink> folderLinks
```
  - OWNER_FILTER_FOLDERLINKS
```
public static final java.lang.String OWNER_FILTER_FOLDERLINKS
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER_FOLDERLINKS
```
public static final java.lang.String GROUP_FILTER_FOLDERLINKS
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER_FOLDERLINKS
```
public static final java.lang.String EVENT_FILTER_FOLDERLINKS
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER_FOLDERLINKS
```
public static final java.lang.String PERMS_FILTER_FOLDERLINKS
```
    See Also:
    
    Constant Field Values
  - annotationLinks
```
protected java.util.Set<RoiAnnotationLink> annotationLinks
```
  - OWNER_FILTER_ANNOTATIONLINKS
```
public static final java.lang.String OWNER_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - GROUP_FILTER_ANNOTATIONLINKS
```
public static final java.lang.String GROUP_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - EVENT_FILTER_ANNOTATIONLINKS
```
public static final java.lang.String EVENT_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - PERMS_FILTER_ANNOTATIONLINKS
```
public static final java.lang.String PERMS_FILTER_ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - description
```
protected java.lang.String description
```
  - details
```
protected Details details
```
  - NAME
```
public static final java.lang.String NAME
```
    See Also:
    
    Constant Field Values
  - SHAPES
```
public static final java.lang.String SHAPES
```
    See Also:
    
    Constant Field Values
  - IMAGE
```
public static final java.lang.String IMAGE
```
    See Also:
    
    Constant Field Values
  - SOURCE
```
public static final java.lang.String SOURCE
```
    See Also:
    
    Constant Field Values
  - FOLDERLINKSCOUNTPEROWNER
```
public static final java.lang.String FOLDERLINKSCOUNTPEROWNER
```
    See Also:
    
    Constant Field Values
  - FOLDERLINKS
```
public static final java.lang.String FOLDERLINKS
```
    See Also:
    
    Constant Field Values
  - ANNOTATIONLINKSCOUNTPEROWNER
```
public static final java.lang.String ANNOTATIONLINKSCOUNTPEROWNER
```
    See Also:
    
    Constant Field Values
  - ANNOTATIONLINKS
```
public static final java.lang.String ANNOTATIONLINKS
```
    See Also:
    
    Constant Field Values
  - DESCRIPTION
```
public static final java.lang.String DESCRIPTION
```
    See Also:
    
    Constant Field Values
  - DETAILS
```
public static final java.lang.String DETAILS
```
    See Also:
    
    Constant Field Values
  - FIELDS
```
public static final java.util.Set<java.lang.String> FIELDS
```
  - _dynamicFields
```
protected java.util.Map<java.lang.String,java.lang.Object> _dynamicFields
```
  - _loaded
```
protected boolean _loaded
```
- Constructor Detail
  - Roi
```
public Roi()
```
  - Roi
```
protected Roi(java.lang.Long id)
```
  - Roi
```
public Roi(java.lang.Long id,
           boolean loaded)
```
    Main constructor.
- Method Detail
  - getId
```
@DocumentId
public java.lang.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(java.lang.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 java.lang.Integer getVersion()
```
    This version number is controlled by the database for optimisitic locking.
    
    Specified by:
    
    getVersion in interface IMutable
  - setVersion
```
public void setVersion(java.lang.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.
  - getName
```
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getName()
```
    Simple field ome.model.roi.Roi.name (java.lang.String)
  - setName
```
public void setName(java.lang.String name)
```
  - getShapes
```
protected java.util.List<Shape> getShapes()
```
    returns shapes . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many List ome.model.roi.Roi.shapes (ome.model.roi.Shape) Values are indexed by the column "index" on ome.model.roi.Shape
  - setShapes
```
protected void setShapes(java.util.List<Shape> shapes)
```
    setter for shapes should be avoided. Does not fulfill normal semantics.
  - sizeOfShapes
```
public int sizeOfShapes()
```
    returns the size of shapes. If less than zero, the Set was null.
  - iterateShapes
```
public java.util.Iterator<Shape> iterateShapes()
```
    should be used rather than accessing the shapes set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfShapes() is less than zero.
  - unmodifiableShapes
```
public java.util.Collection<Shape> unmodifiableShapes()
```
    Returns an unmodifiable collection-view
  - collectShapes
```
public <E> java.util.List<E> collectShapes(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.roi.Shape while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateShapes() internally and so will return a value even if the underlying collection is null.
  - addShape
```
public void addShape(Shape target)
```
    use instead of setShapes . Makes the necessary call on ome.model.roi.Shape as well.
  - addShapeSet
```
public void addShapeSet(java.util.Collection<Shape> targets)
```
    use like addShape.
  - removeShape
```
public void removeShape(Shape target)
```
    removes a single element from this set and makes the inverse call on ome.model.roi.Shape
  - removeShapeSet
```
public void removeShapeSet(java.util.Collection<Shape> targets)
```
    use like removeShape
  - clearShapes
```
public void clearShapes()
```
    clears the set.
  - getShape
```
public Shape getShape(int index)
               throws java.lang.IndexOutOfBoundsException
```
    Gets the ome.model.roi.Shape at the given index.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException
  - setShape
```
public Shape setShape(int index,
                      Shape element)
               throws java.lang.IndexOutOfBoundsException
```
    Sets the ome.model.roi.Shape at the given index. Adheres to the List.set(int, Object) contract. To extend the list, use addShape(Shape).
    
    Throws:
    
    java.lang.IndexOutOfBoundsException
    
    See Also:
    
    List.set(int, Object)
  - getPrimaryShape
```
public Shape getPrimaryShape()
                      throws java.lang.IndexOutOfBoundsException
```
    Gets the first element of shapes which can be interpreted as the primary or default element in some situations. If there is not first element, an IndexOutOfBoundsException is throws. This method will also throw an ApiUsageException if the collection is unloaded. See sizeOfShapes() for more information.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException
  - setPrimaryShape
```
public Shape setPrimaryShape(Shape element)
                      throws java.lang.IndexOutOfBoundsException
```
    Swaps the first element of shapes with the first instance of the given element. If the given element is not in the list, an IndexOutOfBoundsException will be thrown. Returns the swapped element. This method will also throw an ApiUsageException if the collection is unloaded. See sizeOfShapes() for more information.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException
  - getImage
```
public Image getImage()
```
    Many-to-one field ome.model.roi.Roi.image (ome.model.core.Image)
  - setImage
```
public void setImage(Image image)
```
  - getSource
```
public OriginalFile getSource()
```
    Many-to-one field ome.model.roi.Roi.source (ome.model.core.OriginalFile)
  - setSource
```
public void setSource(OriginalFile source)
```
  - getFolderLinks
```
protected java.util.Set<FolderRoiLink> getFolderLinks()
```
    returns folderLinks . You should not modify this collection unless you know what you are doing. Use the iterate method instead. one-to-many Set ome.model.roi.Roi.folderLinks (ome.model.containers.FolderRoiLink)
  - setFolderLinks
```
protected void setFolderLinks(java.util.Set<FolderRoiLink> folderLinks)
```
    setter for folderLinks should be avoided. Does not fulfill normal semantics.
  - sizeOfFolderLinks
```
public int sizeOfFolderLinks()
```
    returns the size of folderLinks. If less than zero, the Set was null.
  - iterateFolderLinks
```
public java.util.Iterator<FolderRoiLink> iterateFolderLinks()
```
    should be used rather than accessing the folderLinks set directly. This method will never return null, but rather will return an instance of EmptyIterator. To test for a null collection, see of sizeOfFolderLinks() is less than zero.
  - unmodifiableFolderLinks
```
public java.util.Collection<FolderRoiLink> unmodifiableFolderLinks()
```
    Returns an unmodifiable collection-view
  - collectFolderLinks
```
public <E> java.util.List<E> collectFolderLinks(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.containers.FolderRoiLink while collecting the results. If block == null, then the iterator values themselves are collected. This method uses iterateFolderLinks() internally and so will return a value even if the underlying collection is null.
  - addFolderRoiLink
```
public void addFolderRoiLink(FolderRoiLink target)
```
    use instead of setFolderLinks . Makes the necessary call on ome.model.containers.FolderRoiLink as well.
  - addFolderRoiLinkSet
```
public void addFolderRoiLinkSet(java.util.Collection<FolderRoiLink> targets)
```
    use like addFolderRoiLink.
  - removeFolderRoiLink
```
public void removeFolderRoiLink(FolderRoiLink target)
```
    removes a single element from this set and makes the inverse call on ome.model.containers.FolderRoiLink
  - removeFolderRoiLinkSet
```
public void removeFolderRoiLinkSet(java.util.Collection<FolderRoiLink> targets)
```
    use like removeFolderRoiLink
  - linkFolder
```
public FolderRoiLink linkFolder(Folder addition)
```
    Adds a ome.model.containers.FolderRoiLink to folderLinks . This entails changing our folderLinks Set, creating a new ome.model.containers.FolderRoiLink and calling linkFolder on the ome.model.containers.Folder.
  - addFolderRoiLink
```
public void addFolderRoiLink(FolderRoiLink link,
                             boolean bothSides)
```
    Adds a ome.model.containers.FolderRoiLink to folderLinks, allowing for recursion -- whether or not addFolderRoiLink will be called on the addition if it is loaded
  - linkedFolderIterator
```
public java.util.Iterator<Folder> linkedFolderIterator()
```
    provides an iterator over the child values of the folderLinks. Like with most Collection iterators, modifications to the underlying collection while iterating will result in an ConcurrentModificationException. Use linkedFolderList() instead.
  - findFolderRoiLink
```
public java.util.Set<FolderRoiLink> findFolderRoiLink(Folder target)
```
    find all ome.model.containers.FolderRoiLink which have the argument as their parent.
  - linkedFolderList
```
public java.util.List<Folder> linkedFolderList()
```
    produces a List-copy of the underlying collection. Unlike, linkedFolderIterator(), while using the returned List, modifications can be made to the underlying collection without throwing ConcurrentModificationException.
  - eachLinkedFolder
```
public <E> java.util.List<E> eachLinkedFolder(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.containers.Folder while collecting the results. If block == null, then the iterator values themselves are collected.
  - unlinkFolder
```
public void unlinkFolder(Folder removal)
```
    unlinks all ome.model.containers.Folder instances from this instance.
  - removeFolderRoiLink
```
public void removeFolderRoiLink(FolderRoiLink link,
                                boolean bothSides)
```
    removes the given FolderRoiLink from folderLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.
  - clearFolderLinks
```
public void clearFolderLinks()
```
    clears the set.
  - setFolderLinksCountPerOwner
```
protected void setFolderLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
```
  - getFolderLinksCountPerOwner
```
public java.util.Map<java.lang.Long,java.lang.Long> getFolderLinksCountPerOwner()
```
    If fetched, returns the count(*) of ome.model.containers.FolderRoiLink that a user has. If unfetched, returns null. No entries in the collection should be null.
  - getAnnotationLinks
```
protected java.util.Set<RoiAnnotationLink> 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.roi.Roi.annotationLinks (ome.model.annotations.RoiAnnotationLink)
  - setAnnotationLinks
```
protected void setAnnotationLinks(java.util.Set<RoiAnnotationLink> 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 java.util.Iterator<RoiAnnotationLink> 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 java.util.Collection<RoiAnnotationLink> unmodifiableAnnotationLinks()
```
    Returns an unmodifiable collection-view
    
    Specified by:
    
    unmodifiableAnnotationLinks in interface IAnnotated
  - collectAnnotationLinks
```
public <E> java.util.List<E> collectAnnotationLinks(CBlock<E> block)
```
    takes a CBlock and calls the block once for each ome.model.annotations.RoiAnnotationLink 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
  - addRoiAnnotationLink
```
public void addRoiAnnotationLink(RoiAnnotationLink target)
```
    use instead of setAnnotationLinks . Makes the necessary call on ome.model.annotations.RoiAnnotationLink as well.
  - addRoiAnnotationLinkSet
```
public void addRoiAnnotationLinkSet(java.util.Collection<RoiAnnotationLink> targets)
```
    use like addRoiAnnotationLink.
  - removeRoiAnnotationLink
```
public void removeRoiAnnotationLink(RoiAnnotationLink target)
```
    removes a single element from this set and makes the inverse call on ome.model.annotations.RoiAnnotationLink
  - removeRoiAnnotationLinkSet
```
public void removeRoiAnnotationLinkSet(java.util.Collection<RoiAnnotationLink> targets)
```
    use like removeRoiAnnotationLink
  - linkAnnotation
```
public RoiAnnotationLink linkAnnotation(Annotation addition)
```
    Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks . This entails changing our annotationLinks Set, creating a new ome.model.annotations.RoiAnnotationLink and calling linkAnnotation on the ome.model.annotations.Annotation.
    
    Specified by:
    
    linkAnnotation in interface IAnnotated
  - addRoiAnnotationLink
```
public void addRoiAnnotationLink(RoiAnnotationLink link,
                                 boolean bothSides)
```
    Adds a ome.model.annotations.RoiAnnotationLink to annotationLinks, allowing for recursion -- whether or not addRoiAnnotationLink will be called on the addition if it is loaded
  - linkedAnnotationIterator
```
public java.util.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
  - findRoiAnnotationLink
```
public java.util.Set<RoiAnnotationLink> findRoiAnnotationLink(Annotation target)
```
    find all ome.model.annotations.RoiAnnotationLink which have the argument as their child.
  - linkedAnnotationList
```
public java.util.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> java.util.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
  - removeRoiAnnotationLink
```
public void removeRoiAnnotationLink(RoiAnnotationLink link,
                                    boolean bothSides)
```
    removes the given RoiAnnotationLink from annotationLinks, allowing for recursion -- whether or not the removal will call unlinkRoi again if loaded.
  - clearAnnotationLinks
```
public void clearAnnotationLinks()
```
    clears the set.
    
    Specified by:
    
    clearAnnotationLinks in interface IAnnotated
  - setAnnotationLinksCountPerOwner
```
protected void setAnnotationLinksCountPerOwner(java.util.Map<java.lang.Long,java.lang.Long> map)
```
  - getAnnotationLinksCountPerOwner
```
public java.util.Map<java.lang.Long,java.lang.Long> getAnnotationLinksCountPerOwner()
```
    If fetched, returns the count(*) of ome.model.annotations.RoiAnnotationLink that a user has. If unfetched, returns null. No entries in the collection should be null.
  - getDescription
```
@Field(index=TOKENIZED) @Field(index=TOKENIZED,analyzer=@Analyzer(impl=ConfiguredAnalyzer.class),name="combined_fields")
public java.lang.String getDescription()
```
    Simple field ome.model.roi.Roi.description (java.lang.String)
  - setDescription
```
public void setDescription(java.lang.String description)
```
  - 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 subclass of the Details type.
    
    Specified by:
    
    getDetails in interface IObject
  - setDetails
```
protected void setDetails(Details details)
```
  - 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.
  - newInstance
```
public Roi newInstance()
```
  - proxy
```
public Roi proxy()
```
  - acceptFilter
```
public boolean acceptFilter(Filter __filter)
```
    Specified by:
    
    acceptFilter in interface Filterable
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - fields
```
public java.util.Set<java.lang.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 java.lang.Object retrieve(java.lang.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(java.lang.String field,
                  java.lang.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(java.lang.String propertyName)
```

Class Roi

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

name

shapes

OWNER_FILTER_SHAPES

GROUP_FILTER_SHAPES

EVENT_FILTER_SHAPES

PERMS_FILTER_SHAPES

image

source

folderLinks

OWNER_FILTER_FOLDERLINKS

GROUP_FILTER_FOLDERLINKS

EVENT_FILTER_FOLDERLINKS

PERMS_FILTER_FOLDERLINKS

annotationLinks

OWNER_FILTER_ANNOTATIONLINKS

GROUP_FILTER_ANNOTATIONLINKS

EVENT_FILTER_ANNOTATIONLINKS

PERMS_FILTER_ANNOTATIONLINKS

description

details

NAME

SHAPES

IMAGE

SOURCE

FOLDERLINKSCOUNTPEROWNER

FOLDERLINKS

ANNOTATIONLINKSCOUNTPEROWNER

ANNOTATIONLINKS

DESCRIPTION

DETAILS

FIELDS

_dynamicFields

_loaded

Constructor Detail

Roi

Roi

Roi

Method Detail

getId

setId

getVersion

setVersion

getName

setName

getShapes

setShapes

sizeOfShapes

iterateShapes

unmodifiableShapes

collectShapes

addShape

addShapeSet

removeShape

removeShapeSet

clearShapes

getShape

setShape

getPrimaryShape

setPrimaryShape

getImage

setImage

getSource

setSource

getFolderLinks

setFolderLinks