ome.xml.model

Class TypeAnnotation

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Annotation

ome.xml.model.TypeAnnotation

All Implemented Interfaces:

OMEModelObject

Direct Known Subclasses:

FileAnnotation

public abstract class TypeAnnotation
extends Annotation

Field Summary

Fields

Modifier and Type	Field and Description
private static org.slf4j.Logger	LOGGER Logger for this class.
static String	NAMESPACE

Constructor Summary

Constructors

Constructor and Description
TypeAnnotation() Default constructor.
TypeAnnotation(Element element, OMEModel model) Constructs TypeAnnotation recursively from an XML DOM tree.
TypeAnnotation(TypeAnnotation 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 TypeAnnotation_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
void	update(Element element, OMEModel model) Updates TypeAnnotation recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.Annotation

copyLinkedAnnotationList, copyLinkedChannelList, copyLinkedDatasetList, copyLinkedDetectorList, copyLinkedDichroicList, copyLinkedExperimenterGroupList, copyLinkedExperimenterList, copyLinkedFilterList, copyLinkedImageList, copyLinkedInstrumentList, copyLinkedLightPathList, copyLinkedLightSourceList, copyLinkedObjectiveList, copyLinkedPlaneList, copyLinkedPlateAcquisitionList, copyLinkedPlateList, copyLinkedProjectList, copyLinkedReagentList, copyLinkedROIList, copyLinkedScreenList, copyLinkedShapeList, copyLinkedWellList, getAnnotator, getDescription, getID, getLinkedAnnotation, getLinkedChannel, getLinkedDataset, getLinkedDetector, getLinkedDichroic, getLinkedExperimenter, getLinkedExperimenterGroup, getLinkedFilter, getLinkedImage, getLinkedInstrument, getLinkedLightPath, getLinkedLightSource, getLinkedObjective, getLinkedPlane, getLinkedPlate, getLinkedPlateAcquisition, getLinkedProject, getLinkedReagent, getLinkedROI, getLinkedScreen, getLinkedShape, getLinkedWell, getNamespace, linkAnnotation, linkChannel, linkDataset, linkDetector, linkDichroic, linkExperimenter, linkExperimenterGroup, linkFilter, linkImage, linkInstrument, linkLightPath, linkLightSource, linkObjective, linkPlane, linkPlate, linkPlateAcquisition, linkProject, linkReagent, linkROI, linkScreen, linkShape, linkWell, setAnnotator, setDescription, setID, setLinkedAnnotation, setLinkedChannel, setLinkedDataset, setLinkedDetector, setLinkedDichroic, setLinkedExperimenter, setLinkedExperimenterGroup, setLinkedFilter, setLinkedImage, setLinkedInstrument, setLinkedLightPath, setLinkedLightSource, setLinkedObjective, setLinkedPlane, setLinkedPlate, setLinkedPlateAcquisition, setLinkedProject, setLinkedReagent, setLinkedROI, setLinkedScreen, setLinkedShape, setLinkedWell, setNamespace, sizeOfLinkedAnnotationList, sizeOfLinkedChannelList, sizeOfLinkedDatasetList, sizeOfLinkedDetectorList, sizeOfLinkedDichroicList, sizeOfLinkedExperimenterGroupList, sizeOfLinkedExperimenterList, sizeOfLinkedFilterList, sizeOfLinkedImageList, sizeOfLinkedInstrumentList, sizeOfLinkedLightPathList, sizeOfLinkedLightSourceList, sizeOfLinkedObjectiveList, sizeOfLinkedPlaneList, sizeOfLinkedPlateAcquisitionList, sizeOfLinkedPlateList, sizeOfLinkedProjectList, sizeOfLinkedReagentList, sizeOfLinkedROIList, sizeOfLinkedScreenList, sizeOfLinkedShapeList, sizeOfLinkedWellList, unlinkAnnotation, unlinkChannel, unlinkDataset, unlinkDetector, unlinkDichroic, unlinkExperimenter, unlinkExperimenterGroup, unlinkFilter, unlinkImage, unlinkInstrument, unlinkLightPath, unlinkLightSource, unlinkObjective, unlinkPlane, unlinkPlate, unlinkPlateAcquisition, unlinkProject, unlinkReagent, unlinkROI, unlinkScreen, unlinkShape, unlinkWell

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.

Constructor Detail

TypeAnnotation

public TypeAnnotation()

Default constructor.

TypeAnnotation

public TypeAnnotation(Element element,
              OMEModel model)
               throws EnumerationException

Constructs TypeAnnotation 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.

TypeAnnotation

public TypeAnnotation(TypeAnnotation orig)

Copy constructor.

Method Detail

update

public void update(Element element,
          OMEModel model)
            throws EnumerationException

Updates TypeAnnotation 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 Annotation

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 Annotation

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.

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

Overrides:

asXMLElement in class Annotation

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 TypeAnnotation_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 Annotation

Parameters:

document - Destination document for element creation, etc.

TypeAnnotation_element - Element from the subclass. If null a new element will be created of this class.

Returns:

element populated with properties from this class.