ome.xml.model

Class ROI

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
static String	NAMESPACE

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

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.