Package ome.xml.model

Class OME

All Implemented Interfaces:
OMEModelObject
Direct Known Subclasses:
OMEXMLMetadataRoot

public class OME extends AbstractOMEModelObject
  • Field Details

  • Constructor Details

    • 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 Details

    • 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()
    • copyExperimentList

      public List<Experiment> copyExperimentList()
    • clearExperimentList

      public void clearExperimentList()
    • 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 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()
    • copyExperimenterList

      public List<Experimenter> copyExperimenterList()
    • clearExperimenterList

      public void clearExperimenterList()
    • 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 List<ExperimenterGroup> copyExperimenterGroupList()
    • clearExperimenterGroupList

      public void clearExperimenterGroupList()
    • 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 List<Instrument> copyInstrumentList()
    • clearInstrumentList

      public void clearInstrumentList()
    • 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 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)
    • getStructuredAnnotations

      public StructuredAnnotations getStructuredAnnotations()
    • 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)
      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 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.