Package ome.xml.model

Class StructuredAnnotations

java.lang.Object
ome.xml.model.AbstractOMEModelObject
ome.xml.model.StructuredAnnotations
All Implemented Interfaces:
OMEModelObject

public class StructuredAnnotations extends AbstractOMEModelObject
  • Field Details

  • Constructor Details

    • StructuredAnnotations

      public StructuredAnnotations()
      Default constructor.
    • StructuredAnnotations

      public StructuredAnnotations(Element element, OMEModel model) throws EnumerationException
      Constructs StructuredAnnotations 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.
    • StructuredAnnotations

      public StructuredAnnotations(StructuredAnnotations orig)
      Copy constructor.
  • Method Details

    • update

      public void update(Element element, OMEModel model) throws EnumerationException
      Updates StructuredAnnotations 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.
    • sizeOfXMLAnnotationList

      public int sizeOfXMLAnnotationList()
    • copyXMLAnnotationList

      public List<XMLAnnotation> copyXMLAnnotationList()
    • clearXMLAnnotationList

      public void clearXMLAnnotationList()
    • getXMLAnnotation

      public XMLAnnotation getXMLAnnotation(int index)
    • setXMLAnnotation

      public XMLAnnotation setXMLAnnotation(int index, XMLAnnotation xmlAnnotation)
    • addXMLAnnotation

      public void addXMLAnnotation(XMLAnnotation xmlAnnotation)
    • removeXMLAnnotation

      public void removeXMLAnnotation(XMLAnnotation xmlAnnotation)
    • sizeOfFileAnnotationList

      public int sizeOfFileAnnotationList()
    • copyFileAnnotationList

      public List<FileAnnotation> copyFileAnnotationList()
    • clearFileAnnotationList

      public void clearFileAnnotationList()
    • getFileAnnotation

      public FileAnnotation getFileAnnotation(int index)
    • setFileAnnotation

      public FileAnnotation setFileAnnotation(int index, FileAnnotation fileAnnotation)
    • addFileAnnotation

      public void addFileAnnotation(FileAnnotation fileAnnotation)
    • removeFileAnnotation

      public void removeFileAnnotation(FileAnnotation fileAnnotation)
    • sizeOfListAnnotationList

      public int sizeOfListAnnotationList()
    • copyListAnnotationList

      public List<ListAnnotation> copyListAnnotationList()
    • clearListAnnotationList

      public void clearListAnnotationList()
    • getListAnnotation

      public ListAnnotation getListAnnotation(int index)
    • setListAnnotation

      public ListAnnotation setListAnnotation(int index, ListAnnotation listAnnotation)
    • addListAnnotation

      public void addListAnnotation(ListAnnotation listAnnotation)
    • removeListAnnotation

      public void removeListAnnotation(ListAnnotation listAnnotation)
    • sizeOfLongAnnotationList

      public int sizeOfLongAnnotationList()
    • copyLongAnnotationList

      public List<LongAnnotation> copyLongAnnotationList()
    • clearLongAnnotationList

      public void clearLongAnnotationList()
    • getLongAnnotation

      public LongAnnotation getLongAnnotation(int index)
    • setLongAnnotation

      public LongAnnotation setLongAnnotation(int index, LongAnnotation longAnnotation)
    • addLongAnnotation

      public void addLongAnnotation(LongAnnotation longAnnotation)
    • removeLongAnnotation

      public void removeLongAnnotation(LongAnnotation longAnnotation)
    • sizeOfDoubleAnnotationList

      public int sizeOfDoubleAnnotationList()
    • copyDoubleAnnotationList

      public List<DoubleAnnotation> copyDoubleAnnotationList()
    • clearDoubleAnnotationList

      public void clearDoubleAnnotationList()
    • getDoubleAnnotation

      public DoubleAnnotation getDoubleAnnotation(int index)
    • setDoubleAnnotation

      public DoubleAnnotation setDoubleAnnotation(int index, DoubleAnnotation doubleAnnotation)
    • addDoubleAnnotation

      public void addDoubleAnnotation(DoubleAnnotation doubleAnnotation)
    • removeDoubleAnnotation

      public void removeDoubleAnnotation(DoubleAnnotation doubleAnnotation)
    • sizeOfCommentAnnotationList

      public int sizeOfCommentAnnotationList()
    • copyCommentAnnotationList

      public List<CommentAnnotation> copyCommentAnnotationList()
    • clearCommentAnnotationList

      public void clearCommentAnnotationList()
    • getCommentAnnotation

      public CommentAnnotation getCommentAnnotation(int index)
    • setCommentAnnotation

      public CommentAnnotation setCommentAnnotation(int index, CommentAnnotation commentAnnotation)
    • addCommentAnnotation

      public void addCommentAnnotation(CommentAnnotation commentAnnotation)
    • removeCommentAnnotation

      public void removeCommentAnnotation(CommentAnnotation commentAnnotation)
    • sizeOfBooleanAnnotationList

      public int sizeOfBooleanAnnotationList()
    • copyBooleanAnnotationList

      public List<BooleanAnnotation> copyBooleanAnnotationList()
    • clearBooleanAnnotationList

      public void clearBooleanAnnotationList()
    • getBooleanAnnotation

      public BooleanAnnotation getBooleanAnnotation(int index)
    • setBooleanAnnotation

      public BooleanAnnotation setBooleanAnnotation(int index, BooleanAnnotation booleanAnnotation)
    • addBooleanAnnotation

      public void addBooleanAnnotation(BooleanAnnotation booleanAnnotation)
    • removeBooleanAnnotation

      public void removeBooleanAnnotation(BooleanAnnotation booleanAnnotation)
    • sizeOfTimestampAnnotationList

      public int sizeOfTimestampAnnotationList()
    • copyTimestampAnnotationList

      public List<TimestampAnnotation> copyTimestampAnnotationList()
    • clearTimestampAnnotationList

      public void clearTimestampAnnotationList()
    • getTimestampAnnotation

      public TimestampAnnotation getTimestampAnnotation(int index)
    • setTimestampAnnotation

      public TimestampAnnotation setTimestampAnnotation(int index, TimestampAnnotation timestampAnnotation)
    • addTimestampAnnotation

      public void addTimestampAnnotation(TimestampAnnotation timestampAnnotation)
    • removeTimestampAnnotation

      public void removeTimestampAnnotation(TimestampAnnotation timestampAnnotation)
    • sizeOfTagAnnotationList

      public int sizeOfTagAnnotationList()
    • copyTagAnnotationList

      public List<TagAnnotation> copyTagAnnotationList()
    • clearTagAnnotationList

      public void clearTagAnnotationList()
    • getTagAnnotation

      public TagAnnotation getTagAnnotation(int index)
    • setTagAnnotation

      public TagAnnotation setTagAnnotation(int index, TagAnnotation tagAnnotation)
    • addTagAnnotation

      public void addTagAnnotation(TagAnnotation tagAnnotation)
    • removeTagAnnotation

      public void removeTagAnnotation(TagAnnotation tagAnnotation)
    • sizeOfTermAnnotationList

      public int sizeOfTermAnnotationList()
    • copyTermAnnotationList

      public List<TermAnnotation> copyTermAnnotationList()
    • clearTermAnnotationList

      public void clearTermAnnotationList()
    • getTermAnnotation

      public TermAnnotation getTermAnnotation(int index)
    • setTermAnnotation

      public TermAnnotation setTermAnnotation(int index, TermAnnotation termAnnotation)
    • addTermAnnotation

      public void addTermAnnotation(TermAnnotation termAnnotation)
    • removeTermAnnotation

      public void removeTermAnnotation(TermAnnotation termAnnotation)
    • sizeOfMapAnnotationList

      public int sizeOfMapAnnotationList()
    • copyMapAnnotationList

      public List<MapAnnotation> copyMapAnnotationList()
    • clearMapAnnotationList

      public void clearMapAnnotationList()
    • getMapAnnotation

      public MapAnnotation getMapAnnotation(int index)
    • setMapAnnotation

      public MapAnnotation setMapAnnotation(int index, MapAnnotation mapAnnotation)
    • addMapAnnotation

      public void addMapAnnotation(MapAnnotation mapAnnotation)
    • removeMapAnnotation

      public void removeMapAnnotation(MapAnnotation mapAnnotation)
    • 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 StructuredAnnotations_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.
      StructuredAnnotations_element - Element from the subclass. If null a new element will be created of this class.
      Returns:
      element populated with properties from this class.