ome.xml.model

Class FileAnnotation

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Annotation

ome.xml.model.TypeAnnotation

ome.xml.model.FileAnnotation

All Implemented Interfaces:

OMEModelObject

public class FileAnnotation
extends TypeAnnotation

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
FileAnnotation() Default constructor.
FileAnnotation(Element element, OMEModel model) Constructs FileAnnotation recursively from an XML DOM tree.
FileAnnotation(FileAnnotation 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 FileAnnotation_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
BinaryFile	getBinaryFile()
StructuredAnnotations	getStructuredAnnotations()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
void	setBinaryFile(BinaryFile binaryFile)
void	setStructuredAnnotations(StructuredAnnotations structuredAnnotations_BackReference)
void	update(Element element, OMEModel model) Updates FileAnnotation 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.

binaryFile

private BinaryFile binaryFile

structuredAnnotations

private StructuredAnnotations structuredAnnotations

Constructor Detail

FileAnnotation

public FileAnnotation()

Default constructor.

FileAnnotation

public FileAnnotation(Element element,
              OMEModel model)
               throws EnumerationException

Constructs FileAnnotation 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.

FileAnnotation

public FileAnnotation(FileAnnotation orig)

Copy constructor.

Method Detail

update

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

Updates FileAnnotation 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 TypeAnnotation

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 TypeAnnotation

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.

getBinaryFile

public BinaryFile getBinaryFile()

setBinaryFile

public void setBinaryFile(BinaryFile binaryFile)

getStructuredAnnotations

public StructuredAnnotations getStructuredAnnotations()

setStructuredAnnotations

public void setStructuredAnnotations(StructuredAnnotations structuredAnnotations_BackReference)

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 TypeAnnotation

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 FileAnnotation_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 TypeAnnotation

Parameters:

document - Destination document for element creation, etc.

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

Returns:

element populated with properties from this class.