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 Summary

Fields

Modifier and Type	Field and Description
private List<BooleanAnnotation>	booleanAnnotations
private List<CommentAnnotation>	commentAnnotations
private List<DoubleAnnotation>	doubleAnnotations
private List<FileAnnotation>	fileAnnotations
private List<ListAnnotation>	listAnnotations
private static org.slf4j.Logger	LOGGER Logger for this class.
private List<LongAnnotation>	longAnnotations
private List<MapAnnotation>	mapAnnotations
static String	NAMESPACE
private List<TagAnnotation>	tagAnnotations
private List<TermAnnotation>	termAnnotations
private List<TimestampAnnotation>	timestampAnnotations
private List<XMLAnnotation>	xmlAnnotations

Constructor Summary

Constructors

Constructor and Description
StructuredAnnotations() Default constructor.
StructuredAnnotations(Element element, OMEModel model) Constructs StructuredAnnotations recursively from an XML DOM tree.
StructuredAnnotations(StructuredAnnotations orig) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addBooleanAnnotation(BooleanAnnotation booleanAnnotation)
void	addCommentAnnotation(CommentAnnotation commentAnnotation)
void	addDoubleAnnotation(DoubleAnnotation doubleAnnotation)
void	addFileAnnotation(FileAnnotation fileAnnotation)
void	addListAnnotation(ListAnnotation listAnnotation)
void	addLongAnnotation(LongAnnotation longAnnotation)
void	addMapAnnotation(MapAnnotation mapAnnotation)
void	addTagAnnotation(TagAnnotation tagAnnotation)
void	addTermAnnotation(TermAnnotation termAnnotation)
void	addTimestampAnnotation(TimestampAnnotation timestampAnnotation)
void	addXMLAnnotation(XMLAnnotation xmlAnnotation)
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element StructuredAnnotations_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<BooleanAnnotation>	copyBooleanAnnotationList()
List<CommentAnnotation>	copyCommentAnnotationList()
List<DoubleAnnotation>	copyDoubleAnnotationList()
List<FileAnnotation>	copyFileAnnotationList()
List<ListAnnotation>	copyListAnnotationList()
List<LongAnnotation>	copyLongAnnotationList()
List<MapAnnotation>	copyMapAnnotationList()
List<TagAnnotation>	copyTagAnnotationList()
List<TermAnnotation>	copyTermAnnotationList()
List<TimestampAnnotation>	copyTimestampAnnotationList()
List<XMLAnnotation>	copyXMLAnnotationList()
BooleanAnnotation	getBooleanAnnotation(int index)
CommentAnnotation	getCommentAnnotation(int index)
DoubleAnnotation	getDoubleAnnotation(int index)
FileAnnotation	getFileAnnotation(int index)
ListAnnotation	getListAnnotation(int index)
LongAnnotation	getLongAnnotation(int index)
MapAnnotation	getMapAnnotation(int index)
TagAnnotation	getTagAnnotation(int index)
TermAnnotation	getTermAnnotation(int index)
TimestampAnnotation	getTimestampAnnotation(int index)
XMLAnnotation	getXMLAnnotation(int index)
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
void	removeBooleanAnnotation(BooleanAnnotation booleanAnnotation)
void	removeCommentAnnotation(CommentAnnotation commentAnnotation)
void	removeDoubleAnnotation(DoubleAnnotation doubleAnnotation)
void	removeFileAnnotation(FileAnnotation fileAnnotation)
void	removeListAnnotation(ListAnnotation listAnnotation)
void	removeLongAnnotation(LongAnnotation longAnnotation)
void	removeMapAnnotation(MapAnnotation mapAnnotation)
void	removeTagAnnotation(TagAnnotation tagAnnotation)
void	removeTermAnnotation(TermAnnotation termAnnotation)
void	removeTimestampAnnotation(TimestampAnnotation timestampAnnotation)
void	removeXMLAnnotation(XMLAnnotation xmlAnnotation)
BooleanAnnotation	setBooleanAnnotation(int index, BooleanAnnotation booleanAnnotation)
CommentAnnotation	setCommentAnnotation(int index, CommentAnnotation commentAnnotation)
DoubleAnnotation	setDoubleAnnotation(int index, DoubleAnnotation doubleAnnotation)
FileAnnotation	setFileAnnotation(int index, FileAnnotation fileAnnotation)
ListAnnotation	setListAnnotation(int index, ListAnnotation listAnnotation)
LongAnnotation	setLongAnnotation(int index, LongAnnotation longAnnotation)
MapAnnotation	setMapAnnotation(int index, MapAnnotation mapAnnotation)
TagAnnotation	setTagAnnotation(int index, TagAnnotation tagAnnotation)
TermAnnotation	setTermAnnotation(int index, TermAnnotation termAnnotation)
TimestampAnnotation	setTimestampAnnotation(int index, TimestampAnnotation timestampAnnotation)
XMLAnnotation	setXMLAnnotation(int index, XMLAnnotation xmlAnnotation)
int	sizeOfBooleanAnnotationList()
int	sizeOfCommentAnnotationList()
int	sizeOfDoubleAnnotationList()
int	sizeOfFileAnnotationList()
int	sizeOfListAnnotationList()
int	sizeOfLongAnnotationList()
int	sizeOfMapAnnotationList()
int	sizeOfTagAnnotationList()
int	sizeOfTermAnnotationList()
int	sizeOfTimestampAnnotationList()
int	sizeOfXMLAnnotationList()
void	update(Element element, OMEModel model) Updates StructuredAnnotations recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject

getChildrenByTagName, stripNamespacePrefix

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAMESPACE

public static final String NAMESPACE

See Also:

Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

xmlAnnotations

private List<XMLAnnotation> xmlAnnotations

fileAnnotations

private List<FileAnnotation> fileAnnotations

listAnnotations

private List<ListAnnotation> listAnnotations

longAnnotations

private List<LongAnnotation> longAnnotations

doubleAnnotations

private List<DoubleAnnotation> doubleAnnotations

commentAnnotations

private List<CommentAnnotation> commentAnnotations

booleanAnnotations

private List<BooleanAnnotation> booleanAnnotations

timestampAnnotations

private List<TimestampAnnotation> timestampAnnotations

tagAnnotations

private List<TagAnnotation> tagAnnotations

termAnnotations

private List<TermAnnotation> termAnnotations

mapAnnotations

private List<MapAnnotation> mapAnnotations

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.

StructuredAnnotations

public StructuredAnnotations(StructuredAnnotations orig)

Copy constructor.

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()

copyXMLAnnotationList

public List<XMLAnnotation> copyXMLAnnotationList()

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()

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()

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()

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()

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()

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()

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()

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()

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()

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()

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

protected 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.