ome.xml.model

Class OME

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.OME

All Implemented Interfaces:

OMEModelObject

Direct Known Subclasses:

OMEXMLMetadataRoot

public class OME
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	NAMESPACE

Constructor Summary

Constructors

Constructor and Description
OME() Default constructor.
OME(org.w3c.dom.Element element, OMEModel model) Constructs OME recursively from an XML DOM tree.
OME(OME orig) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addDataset(Dataset dataset)
void	addExperiment(Experiment experiment)
void	addExperimenter(Experimenter experimenter)
void	addExperimenterGroup(ExperimenterGroup experimenterGroup)
void	addImage(Image image)
void	addInstrument(Instrument instrument)
void	addPlate(Plate plate)
void	addProject(Project project)
void	addROI(ROI roi)
void	addScreen(Screen screen)
org.w3c.dom.Element	asXMLElement(org.w3c.dom.Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected org.w3c.dom.Element	asXMLElement(org.w3c.dom.Document document, org.w3c.dom.Element OME_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
java.util.List<Dataset>	copyDatasetList()
java.util.List<ExperimenterGroup>	copyExperimenterGroupList()
java.util.List<Experimenter>	copyExperimenterList()
java.util.List<Experiment>	copyExperimentList()
java.util.List<Image>	copyImageList()
java.util.List<Instrument>	copyInstrumentList()
java.util.List<Plate>	copyPlateList()
java.util.List<Project>	copyProjectList()
java.util.List<ROI>	copyROIList()
java.util.List<Screen>	copyScreenList()
BinaryOnly	getBinaryOnly()
java.lang.String	getCreator()
Dataset	getDataset(int index)
Experiment	getExperiment(int index)
Experimenter	getExperimenter(int index)
ExperimenterGroup	getExperimenterGroup(int index)
Image	getImage(int index)
Instrument	getInstrument(int index)
Plate	getPlate(int index)
Project	getProject(int index)
Rights	getRights()
ROI	getROI(int index)
Screen	getScreen(int index)
StructuredAnnotations	getStructuredAnnotations()
java.lang.String	getUUID()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
void	removeDataset(Dataset dataset)
void	removeExperiment(Experiment experiment)
void	removeExperimenter(Experimenter experimenter)
void	removeExperimenterGroup(ExperimenterGroup experimenterGroup)
void	removeImage(Image image)
void	removeInstrument(Instrument instrument)
void	removePlate(Plate plate)
void	removeProject(Project project)
void	removeROI(ROI roi)
void	removeScreen(Screen screen)
void	setBinaryOnly(BinaryOnly binaryOnly)
void	setCreator(java.lang.String creator)
Dataset	setDataset(int index, Dataset dataset)
Experiment	setExperiment(int index, Experiment experiment)
Experimenter	setExperimenter(int index, Experimenter experimenter)
ExperimenterGroup	setExperimenterGroup(int index, ExperimenterGroup experimenterGroup)
Image	setImage(int index, Image image)
Instrument	setInstrument(int index, Instrument instrument)
Plate	setPlate(int index, Plate plate)
Project	setProject(int index, Project project)
void	setRights(Rights rights)
ROI	setROI(int index, ROI roi)
Screen	setScreen(int index, Screen screen)
void	setStructuredAnnotations(StructuredAnnotations structuredAnnotations)
void	setUUID(java.lang.String uuid)
int	sizeOfDatasetList()
int	sizeOfExperimenterGroupList()
int	sizeOfExperimenterList()
int	sizeOfExperimentList()
int	sizeOfImageList()
int	sizeOfInstrumentList()
int	sizeOfPlateList()
int	sizeOfProjectList()
int	sizeOfROIList()
int	sizeOfScreenList()
void	update(org.w3c.dom.Element element, OMEModel model) Updates OME 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 java.lang.String NAMESPACE

See Also:

Constant Field Values

Constructor Detail

OME

public OME()

Default constructor.

OME

public OME(org.w3c.dom.Element element,
   OMEModel model)
    throws EnumerationException

Constructs OME 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.

OME

public OME(OME orig)

Copy constructor.

Method Detail

update

public void update(org.w3c.dom.Element element,
          OMEModel model)
            throws EnumerationException

Updates OME 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.

getUUID

public java.lang.String getUUID()

setUUID

public void setUUID(java.lang.String uuid)

getCreator

public java.lang.String getCreator()

setCreator

public void setCreator(java.lang.String creator)

getRights

public Rights getRights()

setRights

public void setRights(Rights rights)

sizeOfProjectList

public int sizeOfProjectList()

copyProjectList

public java.util.List<Project> copyProjectList()

getProject

public Project getProject(int index)

setProject

public Project setProject(int index,
                 Project project)

addProject

public void addProject(Project project)

removeProject

public void removeProject(Project project)

sizeOfDatasetList

public int sizeOfDatasetList()

copyDatasetList

public java.util.List<Dataset> copyDatasetList()

getDataset

public Dataset getDataset(int index)

setDataset

public Dataset setDataset(int index,
                 Dataset dataset)

addDataset

public void addDataset(Dataset dataset)

removeDataset

public void removeDataset(Dataset dataset)

sizeOfExperimentList

public int sizeOfExperimentList()

copyExperimentList

public java.util.List<Experiment> copyExperimentList()

getExperiment

public Experiment getExperiment(int index)

setExperiment

public Experiment setExperiment(int index,
                       Experiment experiment)

addExperiment

public void addExperiment(Experiment experiment)

removeExperiment

public void removeExperiment(Experiment experiment)

sizeOfPlateList

public int sizeOfPlateList()

copyPlateList

public java.util.List<Plate> copyPlateList()

getPlate

public Plate getPlate(int index)

setPlate

public Plate setPlate(int index,
             Plate plate)

addPlate

public void addPlate(Plate plate)

removePlate

public void removePlate(Plate plate)

sizeOfScreenList

public int sizeOfScreenList()

copyScreenList

public java.util.List<Screen> copyScreenList()

getScreen

public Screen getScreen(int index)

setScreen

public Screen setScreen(int index,
               Screen screen)

addScreen

public void addScreen(Screen screen)

removeScreen

public void removeScreen(Screen screen)

sizeOfExperimenterList

public int sizeOfExperimenterList()

copyExperimenterList

public java.util.List<Experimenter> copyExperimenterList()

getExperimenter

public Experimenter getExperimenter(int index)

setExperimenter

public Experimenter setExperimenter(int index,
                           Experimenter experimenter)

addExperimenter

public void addExperimenter(Experimenter experimenter)

removeExperimenter

public void removeExperimenter(Experimenter experimenter)

sizeOfExperimenterGroupList

public int sizeOfExperimenterGroupList()

copyExperimenterGroupList

public java.util.List<ExperimenterGroup> copyExperimenterGroupList()

getExperimenterGroup

public ExperimenterGroup getExperimenterGroup(int index)

setExperimenterGroup

public ExperimenterGroup setExperimenterGroup(int index,
                                     ExperimenterGroup experimenterGroup)

addExperimenterGroup

public void addExperimenterGroup(ExperimenterGroup experimenterGroup)

removeExperimenterGroup

public void removeExperimenterGroup(ExperimenterGroup experimenterGroup)

sizeOfInstrumentList

public int sizeOfInstrumentList()

copyInstrumentList

public java.util.List<Instrument> copyInstrumentList()

getInstrument

public Instrument getInstrument(int index)

setInstrument

public Instrument setInstrument(int index,
                       Instrument instrument)

addInstrument

public void addInstrument(Instrument instrument)

removeInstrument

public void removeInstrument(Instrument instrument)

sizeOfImageList

public int sizeOfImageList()

copyImageList

public java.util.List<Image> copyImageList()

getImage

public Image getImage(int index)

setImage

public Image setImage(int index,
             Image image)

addImage

public void addImage(Image image)

removeImage

public void removeImage(Image image)

getStructuredAnnotations

public StructuredAnnotations getStructuredAnnotations()

setStructuredAnnotations

public void setStructuredAnnotations(StructuredAnnotations structuredAnnotations)

sizeOfROIList

public int sizeOfROIList()

copyROIList

public java.util.List<ROI> copyROIList()

getROI

public ROI getROI(int index)

setROI

public ROI setROI(int index,
         ROI roi)

addROI

public void addROI(ROI roi)

removeROI

public void removeROI(ROI roi)

getBinaryOnly

public BinaryOnly getBinaryOnly()

setBinaryOnly

public void setBinaryOnly(BinaryOnly binaryOnly)

asXMLElement

public org.w3c.dom.Element asXMLElement(org.w3c.dom.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 org.w3c.dom.Element asXMLElement(org.w3c.dom.Document document,
                               org.w3c.dom.Element OME_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.

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

Returns:

element populated with properties from this class.