Package ome.xml.model

Class OME

    • 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)

      • sizeOfFolderList

        public int sizeOfFolderList()

      • copyFolderList

        public java.util.List<Folder> copyFolderList()

      • 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()

      • copyExperimentList

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

      • getExperiment

        public Experiment getExperiment​(int index)

      • 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)

      • 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)

      • 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)

      • 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)

      • 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

        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 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.