ROI (Bio-Formats API)

java.lang.Object
- ome.xml.model.AbstractOMEModelObject
- - ome.xml.model.ROI

All Implemented Interfaces:: OMEModelObject

public class ROI
extends AbstractOMEModelObject

Field Summary

Fields
Modifier and Type	Field and Description
`private List<Annotation>`	`annotationLinks`
`private String`	`description`
`private String`	`id`
`private List<Image>`	`imageLinks`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`private List<MicrobeamManipulation>`	`microbeamManipulationLinks`
`private String`	`name`
`private String`	`namespace`
`static String`	`NAMESPACE`
`private Union`	`union`

Constructor Summary

Constructors
Constructor and Description
`ROI()` Default constructor.
`ROI(Element element, OMEModel model)` Constructs ROI recursively from an XML DOM tree.
`ROI(ROI orig)` Copy constructor.

Method Summary

Methods
Modifier and Type	Method and Description
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element ROI_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<Annotation>`	`copyLinkedAnnotationList()`
`List<Image>`	`copyLinkedImageList()`
`List<MicrobeamManipulation>`	`copyLinkedMicrobeamManipulationList()`
`String`	`getDescription()`
`String`	`getID()`
`Annotation`	`getLinkedAnnotation(int index)`
`Image`	`getLinkedImage(int index)`
`MicrobeamManipulation`	`getLinkedMicrobeamManipulation(int index)`
`String`	`getName()`
`String`	`getNamespace()`
`Union`	`getUnion()`
`boolean`	`link(Reference reference, OMEModelObject o)` Link a given OME model object to this model object.
`boolean`	`linkAnnotation(Annotation o)`
`boolean`	`linkImage(Image o)`
`boolean`	`linkMicrobeamManipulation(MicrobeamManipulation o)`
`void`	`setDescription(String description)`
`void`	`setID(String id)`
`Annotation`	`setLinkedAnnotation(int index, Annotation o)`
`Image`	`setLinkedImage(int index, Image o)`
`MicrobeamManipulation`	`setLinkedMicrobeamManipulation(int index, MicrobeamManipulation o)`
`void`	`setName(String name)`
`void`	`setNamespace(String namespace)`
`void`	`setUnion(Union union)`
`int`	`sizeOfLinkedAnnotationList()`
`int`	`sizeOfLinkedImageList()`
`int`	`sizeOfLinkedMicrobeamManipulationList()`
`boolean`	`unlinkAnnotation(Annotation o)`
`boolean`	`unlinkImage(Image o)`
`boolean`	`unlinkMicrobeamManipulation(MicrobeamManipulation o)`
`void`	`update(Element element, OMEModel model)` Updates ROI recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject
getChildrenByTagName, stripNamespacePrefix

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

- Field Detail
  - NAMESPACE
```
public static final String NAMESPACE
```
    See Also:
    Constant Field Values
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
    Logger for this class.
  - namespace
```
private String namespace
```
  - id
```
private String id
```
  - name
```
private String name
```
  - union
```
private Union union
```
  - annotationLinks
```
private List<Annotation> annotationLinks
```
  - description
```
private String description
```
  - imageLinks
```
private List<Image> imageLinks
```
  - microbeamManipulationLinks
```
private List<MicrobeamManipulation> microbeamManipulationLinks
```
- Constructor Detail
  - ROI
```
public ROI()
```
    Default constructor.
  - ROI
```
public ROI(Element element,
   OMEModel model)
    throws EnumerationException
```
    Constructs ROI recursively from an XML DOM tree.
    
    Parameters:
    element - Root of the XML DOM tree to construct a model object graph from.
    model - Handler for the OME model which keeps track of instances and references seen during object population.
    
    Throws:
    
    EnumerationException - If there is an error instantiating an enumeration during model object creation.
  - ROI
```
public ROI(ROI orig)
```
    Copy constructor.
- Method Detail
  - update
```
public void update(Element element,
          OMEModel model)
            throws EnumerationException
```
    Updates ROI recursively from an XML DOM tree. NOTE: No properties are removed, only added or updated.
    
    Specified by:
    
    update in interface OMEModelObject
    
    Overrides:
    
    update in class AbstractOMEModelObject
    
    Parameters:
    element - Root of the XML DOM tree to construct a model object graph from.
    model - Handler for the OME model which keeps track of instances and references seen during object population.
    
    Throws:
    
    EnumerationException - If there is an error instantiating an enumeration during model object creation.
  - link
```
public boolean link(Reference reference,
           OMEModelObject o)
```
    Description copied from interface: OMEModelObject
    
    Link a given OME model object to this model object.
    
    Specified by:
    
    link in interface OMEModelObject
    
    Overrides:
    
    link in class AbstractOMEModelObject
    
    Parameters:
    reference - The type qualifier for the reference. This should be the corresponding reference type for o. If, for example, o is of type Image, reference MUST be of type ImageRef.
    o - Model object to link to.
    
    Returns:
    true if this model object was able to handle the reference, false otherwise.
  - getNamespace
```
public String getNamespace()
```
  - setNamespace
```
public void setNamespace(String namespace)
```
  - getID
```
public String getID()
```
  - setID
```
public void setID(String id)
```
  - getName
```
public String getName()
```
  - setName
```
public void setName(String name)
```
  - getUnion
```
public Union getUnion()
```
  - setUnion
```
public void setUnion(Union union)
```
  - sizeOfLinkedAnnotationList
```
public int sizeOfLinkedAnnotationList()
```
  - copyLinkedAnnotationList
```
public List<Annotation> copyLinkedAnnotationList()
```
  - getLinkedAnnotation
```
public Annotation getLinkedAnnotation(int index)
```
  - setLinkedAnnotation
```
public Annotation setLinkedAnnotation(int index,
                             Annotation o)
```
  - linkAnnotation
```
public boolean linkAnnotation(Annotation o)
```
  - unlinkAnnotation
```
public boolean unlinkAnnotation(Annotation o)
```
  - getDescription
```
public String getDescription()
```
  - setDescription
```
public void setDescription(String description)
```
  - sizeOfLinkedImageList
```
public int sizeOfLinkedImageList()
```
  - copyLinkedImageList
```
public List<Image> copyLinkedImageList()
```
  - getLinkedImage
```
public Image getLinkedImage(int index)
```
  - setLinkedImage
```
public Image setLinkedImage(int index,
                   Image o)
```
  - linkImage
```
public boolean linkImage(Image o)
```
  - unlinkImage
```
public boolean unlinkImage(Image o)
```
  - sizeOfLinkedMicrobeamManipulationList
```
public int sizeOfLinkedMicrobeamManipulationList()
```
  - copyLinkedMicrobeamManipulationList
```
public List<MicrobeamManipulation> copyLinkedMicrobeamManipulationList()
```
  - getLinkedMicrobeamManipulation
```
public MicrobeamManipulation getLinkedMicrobeamManipulation(int index)
```
  - setLinkedMicrobeamManipulation
```
public MicrobeamManipulation setLinkedMicrobeamManipulation(int index,
                                                   MicrobeamManipulation o)
```
  - linkMicrobeamManipulation
```
public boolean linkMicrobeamManipulation(MicrobeamManipulation o)
```
  - unlinkMicrobeamManipulation
```
public boolean unlinkMicrobeamManipulation(MicrobeamManipulation o)
```
  - asXMLElement
```
public Element asXMLElement(Document document)
```
    Description copied from interface: OMEModelObject
    
    Takes the entire object hierarchy and produces an XML DOM tree.
    
    Specified by:
    
    asXMLElement in interface OMEModelObject
    
    Specified by:
    
    asXMLElement in class AbstractOMEModelObject
    
    Parameters:
    document - Destination document for element creation, etc.
    
    Returns:
    XML DOM tree root element for this model object.
  - asXMLElement
```
protected Element asXMLElement(Document document,
                   Element ROI_element)
```
    Description copied from class: AbstractOMEModelObject
    
    Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
    
    Overrides:
    
    asXMLElement in class AbstractOMEModelObject
    
    Parameters:
    document - Destination document for element creation, etc.
    ROI_element - Element from the subclass. If null a new element will be created of this class.
    
    Returns:
    element populated with properties from this class.

Class ROI

Field Summary

Constructor Summary

Method Summary

Methods inherited from class ome.xml.model.AbstractOMEModelObject

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

LOGGER

namespace

id

name

union

annotationLinks

description

imageLinks

microbeamManipulationLinks

Constructor Detail

ROI

ROI

ROI

Method Detail

update

link

getNamespace

setNamespace

getID

setID

getName

setName

getUnion

setUnion

sizeOfLinkedAnnotationList

copyLinkedAnnotationList

getLinkedAnnotation

setLinkedAnnotation

linkAnnotation

unlinkAnnotation

getDescription

setDescription

sizeOfLinkedImageList

copyLinkedImageList

getLinkedImage

setLinkedImage

linkImage

unlinkImage

sizeOfLinkedMicrobeamManipulationList

copyLinkedMicrobeamManipulationList

getLinkedMicrobeamManipulation

setLinkedMicrobeamManipulation

linkMicrobeamManipulation

unlinkMicrobeamManipulation

asXMLElement

asXMLElement