Package 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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
NAMESPACE
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Constructor Summary
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Method Summary
Modifier and Type Method Description void
addDataset(Dataset dataset)
void
addExperiment(Experiment experiment)
void
addExperimenter(Experimenter experimenter)
void
addExperimenterGroup(ExperimenterGroup experimenterGroup)
void
addFolder(Folder folder)
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.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<Folder>
copyFolderList()
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)
Folder
getFolder(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
removeFolder(Folder folder)
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)
Folder
setFolder(int index, Folder folder)
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
sizeOfFolderList()
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
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Field Details
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NAMESPACE
public static final java.lang.String NAMESPACE- See Also:
- Constant Field Values
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Constructor Details
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OME
public OME()Default constructor. -
OME
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
Copy constructor.
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Method Details
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update
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
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 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
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setRights
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sizeOfProjectList
public int sizeOfProjectList() -
copyProjectList
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getProject
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setProject
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addProject
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removeProject
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sizeOfDatasetList
public int sizeOfDatasetList() -
copyDatasetList
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getDataset
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setDataset
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addDataset
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removeDataset
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sizeOfFolderList
public int sizeOfFolderList() -
copyFolderList
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getFolder
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setFolder
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addFolder
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removeFolder
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sizeOfExperimentList
public int sizeOfExperimentList() -
copyExperimentList
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getExperiment
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setExperiment
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addExperiment
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removeExperiment
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sizeOfPlateList
public int sizeOfPlateList() -
copyPlateList
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getPlate
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setPlate
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addPlate
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removePlate
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sizeOfScreenList
public int sizeOfScreenList() -
copyScreenList
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getScreen
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setScreen
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addScreen
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removeScreen
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sizeOfExperimenterList
public int sizeOfExperimenterList() -
copyExperimenterList
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getExperimenter
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setExperimenter
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addExperimenter
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removeExperimenter
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sizeOfExperimenterGroupList
public int sizeOfExperimenterGroupList() -
copyExperimenterGroupList
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getExperimenterGroup
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setExperimenterGroup
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addExperimenterGroup
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removeExperimenterGroup
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sizeOfInstrumentList
public int sizeOfInstrumentList() -
copyInstrumentList
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getInstrument
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setInstrument
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addInstrument
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removeInstrument
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sizeOfImageList
public int sizeOfImageList() -
copyImageList
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getImage
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setImage
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addImage
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removeImage
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getStructuredAnnotations
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setStructuredAnnotations
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sizeOfROIList
public int sizeOfROIList() -
copyROIList
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getROI
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setROI
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addROI
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removeROI
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getBinaryOnly
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setBinaryOnly
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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 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 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 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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