Package ome.xml.model

Class OME

    • Constructor Detail

      • OME

        public OME()
        Default constructor.
      • 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.
      • OME

        public OME​(OME orig)
        Copy constructor.
    • Method Detail

      • 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 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 String getUUID()
      • setUUID

        public void setUUID​(String uuid)
      • getCreator

        public String getCreator()
      • setCreator

        public void setCreator​(String creator)
      • getRights

        public Rights getRights()
      • setRights

        public void setRights​(Rights rights)
      • sizeOfProjectList

        public int sizeOfProjectList()
      • copyProjectList

        public List<Project> copyProjectList()
      • clearProjectList

        public void clearProjectList()
      • 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 List<Dataset> copyDatasetList()
      • clearDatasetList

        public void clearDatasetList()
      • 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)
      • sizeOfFolderList

        public int sizeOfFolderList()
      • copyFolderList

        public List<Folder> copyFolderList()
      • clearFolderList

        public void clearFolderList()
      • getFolder

        public Folder getFolder​(int index)
      • setFolder

        public Folder setFolder​(int index,
                                Folder folder)
      • addFolder

        public void addFolder​(Folder folder)
      • removeFolder

        public void removeFolder​(Folder folder)
      • sizeOfExperimentList

        public int sizeOfExperimentList()
      • clearExperimentList

        public void clearExperimentList()
      • getExperiment

        public Experiment getExperiment​(int index)
      • addExperiment

        public void addExperiment​(Experiment experiment)
      • removeExperiment

        public void removeExperiment​(Experiment experiment)
      • sizeOfPlateList

        public int sizeOfPlateList()
      • copyPlateList

        public List<Plate> copyPlateList()
      • clearPlateList

        public void clearPlateList()
      • 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 List<Screen> copyScreenList()
      • clearScreenList

        public void clearScreenList()
      • 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()
      • clearExperimenterList

        public void clearExperimenterList()
      • getExperimenter

        public Experimenter getExperimenter​(int index)
      • addExperimenter

        public void addExperimenter​(Experimenter experimenter)
      • removeExperimenter

        public void removeExperimenter​(Experimenter experimenter)
      • sizeOfExperimenterGroupList

        public int sizeOfExperimenterGroupList()
      • clearExperimenterGroupList

        public void clearExperimenterGroupList()
      • getExperimenterGroup

        public ExperimenterGroup getExperimenterGroup​(int index)
      • addExperimenterGroup

        public void addExperimenterGroup​(ExperimenterGroup experimenterGroup)
      • removeExperimenterGroup

        public void removeExperimenterGroup​(ExperimenterGroup experimenterGroup)
      • sizeOfInstrumentList

        public int sizeOfInstrumentList()
      • clearInstrumentList

        public void clearInstrumentList()
      • getInstrument

        public Instrument getInstrument​(int index)
      • addInstrument

        public void addInstrument​(Instrument instrument)
      • removeInstrument

        public void removeInstrument​(Instrument instrument)
      • sizeOfImageList

        public int sizeOfImageList()
      • copyImageList

        public List<Image> copyImageList()
      • clearImageList

        public void clearImageList()
      • 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)
      • setStructuredAnnotations

        public void setStructuredAnnotations​(StructuredAnnotations structuredAnnotations)
      • sizeOfROIList

        public int sizeOfROIList()
      • copyROIList

        public List<ROI> copyROIList()
      • clearROIList

        public void clearROIList()
      • 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 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 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.