Package ome.xml.model

Class StructuredAnnotations

    • Constructor Detail

      • 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.
    • Method Detail

      • 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()
      • clearXMLAnnotationList

        public void clearXMLAnnotationList()
      • getXMLAnnotation

        public XMLAnnotation getXMLAnnotation​(int index)
      • addXMLAnnotation

        public void addXMLAnnotation​(XMLAnnotation xmlAnnotation)
      • removeXMLAnnotation

        public void removeXMLAnnotation​(XMLAnnotation xmlAnnotation)
      • sizeOfFileAnnotationList

        public int sizeOfFileAnnotationList()
      • clearFileAnnotationList

        public void clearFileAnnotationList()
      • getFileAnnotation

        public FileAnnotation getFileAnnotation​(int index)
      • addFileAnnotation

        public void addFileAnnotation​(FileAnnotation fileAnnotation)
      • removeFileAnnotation

        public void removeFileAnnotation​(FileAnnotation fileAnnotation)
      • sizeOfListAnnotationList

        public int sizeOfListAnnotationList()
      • clearListAnnotationList

        public void clearListAnnotationList()
      • getListAnnotation

        public ListAnnotation getListAnnotation​(int index)
      • addListAnnotation

        public void addListAnnotation​(ListAnnotation listAnnotation)
      • removeListAnnotation

        public void removeListAnnotation​(ListAnnotation listAnnotation)
      • sizeOfLongAnnotationList

        public int sizeOfLongAnnotationList()
      • clearLongAnnotationList

        public void clearLongAnnotationList()
      • getLongAnnotation

        public LongAnnotation getLongAnnotation​(int index)
      • addLongAnnotation

        public void addLongAnnotation​(LongAnnotation longAnnotation)
      • removeLongAnnotation

        public void removeLongAnnotation​(LongAnnotation longAnnotation)
      • sizeOfDoubleAnnotationList

        public int sizeOfDoubleAnnotationList()
      • clearDoubleAnnotationList

        public void clearDoubleAnnotationList()
      • getDoubleAnnotation

        public DoubleAnnotation getDoubleAnnotation​(int index)
      • addDoubleAnnotation

        public void addDoubleAnnotation​(DoubleAnnotation doubleAnnotation)
      • removeDoubleAnnotation

        public void removeDoubleAnnotation​(DoubleAnnotation doubleAnnotation)
      • sizeOfCommentAnnotationList

        public int sizeOfCommentAnnotationList()
      • clearCommentAnnotationList

        public void clearCommentAnnotationList()
      • getCommentAnnotation

        public CommentAnnotation getCommentAnnotation​(int index)
      • addCommentAnnotation

        public void addCommentAnnotation​(CommentAnnotation commentAnnotation)
      • removeCommentAnnotation

        public void removeCommentAnnotation​(CommentAnnotation commentAnnotation)
      • sizeOfBooleanAnnotationList

        public int sizeOfBooleanAnnotationList()
      • clearBooleanAnnotationList

        public void clearBooleanAnnotationList()
      • getBooleanAnnotation

        public BooleanAnnotation getBooleanAnnotation​(int index)
      • addBooleanAnnotation

        public void addBooleanAnnotation​(BooleanAnnotation booleanAnnotation)
      • removeBooleanAnnotation

        public void removeBooleanAnnotation​(BooleanAnnotation booleanAnnotation)
      • sizeOfTimestampAnnotationList

        public int sizeOfTimestampAnnotationList()
      • clearTimestampAnnotationList

        public void clearTimestampAnnotationList()
      • addTimestampAnnotation

        public void addTimestampAnnotation​(TimestampAnnotation timestampAnnotation)
      • removeTimestampAnnotation

        public void removeTimestampAnnotation​(TimestampAnnotation timestampAnnotation)
      • sizeOfTagAnnotationList

        public int sizeOfTagAnnotationList()
      • clearTagAnnotationList

        public void clearTagAnnotationList()
      • getTagAnnotation

        public TagAnnotation getTagAnnotation​(int index)
      • addTagAnnotation

        public void addTagAnnotation​(TagAnnotation tagAnnotation)
      • removeTagAnnotation

        public void removeTagAnnotation​(TagAnnotation tagAnnotation)
      • sizeOfTermAnnotationList

        public int sizeOfTermAnnotationList()
      • clearTermAnnotationList

        public void clearTermAnnotationList()
      • getTermAnnotation

        public TermAnnotation getTermAnnotation​(int index)
      • addTermAnnotation

        public void addTermAnnotation​(TermAnnotation termAnnotation)
      • removeTermAnnotation

        public void removeTermAnnotation​(TermAnnotation termAnnotation)
      • sizeOfMapAnnotationList

        public int sizeOfMapAnnotationList()
      • clearMapAnnotationList

        public void clearMapAnnotationList()
      • getMapAnnotation

        public MapAnnotation getMapAnnotation​(int index)
      • addMapAnnotation

        public void addMapAnnotation​(MapAnnotation mapAnnotation)
      • removeMapAnnotation

        public void removeMapAnnotation​(MapAnnotation mapAnnotation)
      • 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.