Package ome.xml.model
Class OME
- java.lang.Object
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- ome.xml.model.AbstractOMEModelObject
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- ome.xml.model.OME
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- All Implemented Interfaces:
OMEModelObject
- Direct Known Subclasses:
OMEXMLMetadataRoot
public class OME extends AbstractOMEModelObject
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Method Summary
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Methods inherited from class ome.xml.model.AbstractOMEModelObject
getChildrenByTagName, stripNamespacePrefix
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Field Detail
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NAMESPACE
public static final String NAMESPACE
- See Also:
- Constant Field Values
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Constructor Detail
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OME
public OME()
Default constructor.
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OME
public OME(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.
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OME
public OME(OME orig)
Copy constructor.
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Method Detail
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update
public void update(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 interfaceOMEModelObject
- Overrides:
update
in classAbstractOMEModelObject
- 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.
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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 interfaceOMEModelObject
- Overrides:
link
in classAbstractOMEModelObject
- Parameters:
reference
- The type qualifier for the reference. This should be the corresponding reference type foro
. If, for example,o
is of typeImage
,reference
MUST be of typeImageRef
.o
- Model object to link to.- Returns:
true
if this model object was able to handle the reference,false
otherwise.
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getUUID
public String getUUID()
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setUUID
public void setUUID(String uuid)
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getCreator
public String getCreator()
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setCreator
public void setCreator(String creator)
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getRights
public Rights getRights()
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setRights
public void setRights(Rights rights)
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sizeOfProjectList
public int sizeOfProjectList()
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clearProjectList
public void clearProjectList()
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getProject
public Project getProject(int index)
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addProject
public void addProject(Project project)
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removeProject
public void removeProject(Project project)
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sizeOfDatasetList
public int sizeOfDatasetList()
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clearDatasetList
public void clearDatasetList()
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getDataset
public Dataset getDataset(int index)
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addDataset
public void addDataset(Dataset dataset)
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removeDataset
public void removeDataset(Dataset dataset)
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sizeOfFolderList
public int sizeOfFolderList()
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clearFolderList
public void clearFolderList()
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getFolder
public Folder getFolder(int index)
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addFolder
public void addFolder(Folder folder)
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removeFolder
public void removeFolder(Folder folder)
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sizeOfExperimentList
public int sizeOfExperimentList()
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copyExperimentList
public List<Experiment> copyExperimentList()
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clearExperimentList
public void clearExperimentList()
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getExperiment
public Experiment getExperiment(int index)
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setExperiment
public Experiment setExperiment(int index, Experiment experiment)
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addExperiment
public void addExperiment(Experiment experiment)
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removeExperiment
public void removeExperiment(Experiment experiment)
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sizeOfPlateList
public int sizeOfPlateList()
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clearPlateList
public void clearPlateList()
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getPlate
public Plate getPlate(int index)
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addPlate
public void addPlate(Plate plate)
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removePlate
public void removePlate(Plate plate)
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sizeOfScreenList
public int sizeOfScreenList()
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clearScreenList
public void clearScreenList()
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getScreen
public Screen getScreen(int index)
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addScreen
public void addScreen(Screen screen)
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removeScreen
public void removeScreen(Screen screen)
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sizeOfExperimenterList
public int sizeOfExperimenterList()
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copyExperimenterList
public List<Experimenter> copyExperimenterList()
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clearExperimenterList
public void clearExperimenterList()
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getExperimenter
public Experimenter getExperimenter(int index)
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setExperimenter
public Experimenter setExperimenter(int index, Experimenter experimenter)
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addExperimenter
public void addExperimenter(Experimenter experimenter)
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removeExperimenter
public void removeExperimenter(Experimenter experimenter)
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sizeOfExperimenterGroupList
public int sizeOfExperimenterGroupList()
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copyExperimenterGroupList
public List<ExperimenterGroup> copyExperimenterGroupList()
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clearExperimenterGroupList
public void clearExperimenterGroupList()
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getExperimenterGroup
public ExperimenterGroup getExperimenterGroup(int index)
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setExperimenterGroup
public ExperimenterGroup setExperimenterGroup(int index, ExperimenterGroup experimenterGroup)
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addExperimenterGroup
public void addExperimenterGroup(ExperimenterGroup experimenterGroup)
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removeExperimenterGroup
public void removeExperimenterGroup(ExperimenterGroup experimenterGroup)
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sizeOfInstrumentList
public int sizeOfInstrumentList()
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copyInstrumentList
public List<Instrument> copyInstrumentList()
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clearInstrumentList
public void clearInstrumentList()
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getInstrument
public Instrument getInstrument(int index)
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setInstrument
public Instrument setInstrument(int index, Instrument instrument)
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addInstrument
public void addInstrument(Instrument instrument)
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removeInstrument
public void removeInstrument(Instrument instrument)
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sizeOfImageList
public int sizeOfImageList()
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clearImageList
public void clearImageList()
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getImage
public Image getImage(int index)
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addImage
public void addImage(Image image)
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removeImage
public void removeImage(Image image)
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getStructuredAnnotations
public StructuredAnnotations getStructuredAnnotations()
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setStructuredAnnotations
public void setStructuredAnnotations(StructuredAnnotations structuredAnnotations)
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sizeOfROIList
public int sizeOfROIList()
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clearROIList
public void clearROIList()
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getROI
public ROI getROI(int index)
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addROI
public void addROI(ROI roi)
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removeROI
public void removeROI(ROI roi)
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getBinaryOnly
public BinaryOnly getBinaryOnly()
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setBinaryOnly
public void setBinaryOnly(BinaryOnly binaryOnly)
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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 interfaceOMEModelObject
- Specified by:
asXMLElement
in classAbstractOMEModelObject
- Parameters:
document
- Destination document for element creation, etc.- Returns:
- XML DOM tree root element for this model object.
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asXMLElement
public Element asXMLElement(Document document, 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 classAbstractOMEModelObject
- Parameters:
document
- Destination document for element creation, etc.OME_element
- Element from the subclass. Ifnull
a new element will be created of this class.- Returns:
element
populated with properties from this class.
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