XMLAnnotationManager (IQM 3.5 API)

java.lang.Object
- at.mug.iqm.api.gui.roi.XMLAnnotationManager

```
public class XMLAnnotationManager
extends Object
```
This class is responsible for loading and storing entire stacks of IDrawingLayer, or DefaultDrawingLayer respectively.

Since:

3.1

Author:

Philipp Kainz

Field Summary

Fields
Modifier and Type	Field and Description
`private List<DefaultDrawingLayer>`	`allLayers` This is the internal java object for all layers.
`private AnnotationLayers`	`allLayersJAXB` The root element of the serialized layers.
`private JAXBContext`	`jaxbContext`
`private static org.apache.log4j.Logger`	`logger`
`private Marshaller`	`marshaller`
`private ObjectFactory`	`of`
`private Unmarshaller`	`unmarshaller`
`static String`	`XML_DATA_ENCODING`
`private File`	`xmlFile`
`private InputStream`	`xmlSchemaFileIS`
`private String`	`xmlSchemaLocation`

Constructor Summary

Constructors
Constructor and Description
`XMLAnnotationManager()` Standard constructor.
`XMLAnnotationManager(List<DefaultDrawingLayer> allLayers, File xmlFile)` Create an `XMLAnnotationManager` for a specified location.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`RoiSet`	`angleROItoXML(ArrayList<AngleROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `AngleROI`s to XML representation.
`protected List<DefaultDrawingLayer>`	`convertToList(AnnotationLayers root)` Converts the XML mapping format to a `List` of `DefaultDrawingLayer`s.
`protected AnnotationLayers`	`convertToXML(List<DefaultDrawingLayer> allLayers)` Converts a list of `DefaultDrawingLayer` to the XML mapping format.
`RoiSet`	`ellipseROItoXML(ArrayList<EllipseROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `EllipseROI`s to XML representation.
`RoiSet`	`freehandROItoXML(ArrayList<FreehandROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `FreehandROI`s to XML representation.
`List<DefaultDrawingLayer>`	`getAllLayers()` Get the re-assembled list of all layers.
`File`	`getXmlFile()` Get the location of the XML file.
`RoiSet`	`lineROItoXML(ArrayList<LineROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `LineROI`s to XML representation.
`static void`	`main(String[] args)`
`Color`	`parseXML(Color jaxbObject)` Parse a given XML object to a `Color` instance.
`Shape`	`parseXML(Path jaxbPath)` Reconstructs a Shape object according to a given path.
`double[]`	`parseXML(Point jaxbPoint)` Parses a 2D point into its double coordinates.
`BasicStroke`	`parseXML(Stroke jaxbObject)` Parse a given XML object to a `BasicStroke` instance.
`AngleROI`	`parseXMLAngleROI(AngleRoi jaxbObject)` Parse a given XML object to a `AngleROI` instance.
`EllipseROI`	`parseXMLEllipseROI(EllipseRoi jaxbObject)` Parse a given XML object to a `EllipseROI` instance.
`FreehandROI`	`parseXMLFreehandROI(FreehandRoi jaxbObject)` Parse a given XML object to a `FreehandROI` instance.
`LineROI`	`parseXMLLineROI(LineRoi jaxbObject)` Parse a given XML object to a `LineROI` instance.
`PointROI`	`parseXMLPointROI(PointRoi jaxbObject)` Parse a given XML object to a `PointROI` instance.
`PolygonROI`	`parseXMLPolygonROI(PolygonRoi jaxbObject)` Parse a given XML object to a `PolygonROI` instance.
`RectangleROI`	`parseXMLRectangleROI(RectangleRoi jaxbObject)` Parse a given XML object to a `RectangleROI` instance.
`RoiSet`	`pointROItoXML(ArrayList<PointROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `PointROI`s to XML representation.
`RoiSet`	`polygonROItoXML(ArrayList<PolygonROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `PolygonROI`s to XML representation.
`List<IDrawingLayer>`	`read()` Public delegate method for reading the xml file into a `List` of `DefaultDrawingLayer`s.
`protected AnnotationLayers`	`readXML()` Loads the annotation layers from an existing XML file.
`RoiSet`	`rectangleROItoXML(ArrayList<RectangleROI> shapes, RoiSet roiSetJAXB)` Converts the `ArrayList` of `RectangleROI`s to XML representation.
`void`	`setAllLayers(List<DefaultDrawingLayer> allLayers)` Set a list of all layers available for saving.
`void`	`setXmlFile(File xmlFile)` Set the location of the XML file.
`private static void`	`testLoad(File f)`
`Stroke`	`toXML(BasicStroke stroke, Stroke strokeJAXB, String name)` Converts a given `BasicStroke` instance to the serializable form.
`Color`	`toXML(Color c, Color colorJAXB, String name)` Converts a given `Color` instance to the serializable form.
`Data`	`toXML(Object javaObject, Data dataJAXB)`
`Path`	`toXML(PathIterator iter, Path pathJAXB)` Generates an XML representation of the given `PathIterator` object.
`Point`	`toXML(Point2D point, Point pointJAXB, String id)` Converts a `Point2D` to the XML representation.
`Bounds`	`toXML(Rectangle2D bounds, Bounds boundsJAXB)` Converts the boundaries from a `Rectangle2D` to the XML representation.
`private void`	`validate()` Validates the XML file against the defined schema.
`void`	`write()` Converts the set List of `DefaultDrawingLayer`s to XML and writes the file.
`protected void`	`writeXML()` Writes an XML file to the specified path in the file system.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - logger
```
private static final org.apache.log4j.Logger logger
```
  - xmlSchemaLocation
```
private final String xmlSchemaLocation
```
    See Also:
    
    Constant Field Values
  - XML_DATA_ENCODING
```
public static final String XML_DATA_ENCODING
```
    See Also:
    
    Constant Field Values
  - xmlFile
```
private File xmlFile
```
  - xmlSchemaFileIS
```
private InputStream xmlSchemaFileIS
```
  - allLayers
```
private List<DefaultDrawingLayer> allLayers
```
    This is the internal java object for all layers.
  - jaxbContext
```
private JAXBContext jaxbContext
```
  - marshaller
```
private Marshaller marshaller
```
  - unmarshaller
```
private Unmarshaller unmarshaller
```
  - allLayersJAXB
```
private AnnotationLayers allLayersJAXB
```
    The root element of the serialized layers.
  - of
```
private ObjectFactory of
```
- Constructor Detail
  - XMLAnnotationManager
```
public XMLAnnotationManager()
```
    Standard constructor.
  - XMLAnnotationManager
```
public XMLAnnotationManager(List<DefaultDrawingLayer> allLayers,
                            File xmlFile)
```
    Create an XMLAnnotationManager for a specified location.
    
    Parameters:
    
    allLayers -
    
    xmlFile -
- Method Detail
  - getXmlFile
```
public File getXmlFile()
```
    Get the location of the XML file.
    
    Returns:
    
    a file object
  - setXmlFile
```
public void setXmlFile(File xmlFile)
```
    Set the location of the XML file.
    
    Parameters:
    
    xmlFile -
  - setAllLayers
```
public void setAllLayers(List<DefaultDrawingLayer> allLayers)
```
    Set a list of all layers available for saving.
    
    Parameters:
    
    allLayers -
  - getAllLayers
```
public List<DefaultDrawingLayer> getAllLayers()
```
    Get the re-assembled list of all layers.
    
    Returns:
    
    list which can be passed on the the look panel for rendering
  - validate
```
private void validate()
```
    Validates the XML file against the defined schema.
  - writeXML
```
protected void writeXML()
```
    Writes an XML file to the specified path in the file system.
  - write
```
public void write()
           throws JAXBException
```
    Converts the set List of DefaultDrawingLayers to XML and writes the file.
    
    Throws:
    
    JAXBException
  - read
```
public List<IDrawingLayer> read()
                         throws JAXBException
```
    Public delegate method for reading the xml file into a List of DefaultDrawingLayers.
    
    Returns:
    
    the list
    
    Throws:
    
    JAXBException
  - readXML
```
protected AnnotationLayers readXML()
                            throws JAXBException
```
    Loads the annotation layers from an existing XML file. The file is validated against the corresponding XML schema before loading.
    
    Throws:
    
    JAXBException - - if the XML file does not comply with the schema
  - convertToList
```
protected List<DefaultDrawingLayer> convertToList(AnnotationLayers root)
```
    Converts the XML mapping format to a List of DefaultDrawingLayers.
    
    Parameters:
    
    allLayersJAXB -
    
    allLayers -
    
    Returns:
    
    the assembled list of DefaultDrawingLayers
  - parseXMLPointROI
```
public PointROI parseXMLPointROI(PointRoi jaxbObject)
```
    Parse a given XML object to a PointROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLRectangleROI
```
public RectangleROI parseXMLRectangleROI(RectangleRoi jaxbObject)
```
    Parse a given XML object to a RectangleROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLAngleROI
```
public AngleROI parseXMLAngleROI(AngleRoi jaxbObject)
```
    Parse a given XML object to a AngleROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLEllipseROI
```
public EllipseROI parseXMLEllipseROI(EllipseRoi jaxbObject)
```
    Parse a given XML object to a EllipseROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLFreehandROI
```
public FreehandROI parseXMLFreehandROI(FreehandRoi jaxbObject)
```
    Parse a given XML object to a FreehandROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLLineROI
```
public LineROI parseXMLLineROI(LineRoi jaxbObject)
```
    Parse a given XML object to a LineROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXMLPolygonROI
```
public PolygonROI parseXMLPolygonROI(PolygonRoi jaxbObject)
```
    Parse a given XML object to a PolygonROI instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXML
```
public Shape parseXML(Path jaxbPath)
```
    Reconstructs a Shape object according to a given path.
    
    Parameters:
    
    jaxbPath -
    
    Returns:
    
    the Shape
  - parseXML
```
public double[] parseXML(Point jaxbPoint)
```
    Parses a 2D point into its double coordinates.
    
    Parameters:
    
    jaxbPoint -
    
    Returns:
  - parseXML
```
public BasicStroke parseXML(Stroke jaxbObject)
```
    Parse a given XML object to a BasicStroke instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the java object
  - parseXML
```
public Color parseXML(Color jaxbObject)
```
    Parse a given XML object to a Color instance.
    
    Parameters:
    
    jaxbObject - the XML object
    
    Returns:
    
    the Java object
  - convertToXML
```
protected AnnotationLayers convertToXML(List<DefaultDrawingLayer> allLayers)
```
    Converts a list of DefaultDrawingLayer to the XML mapping format.
    
    Parameters:
    
    allLayers -
    
    allLayersJAXB -
    
    Returns:
    
    the XML representation ready for serialization
  - angleROItoXML
```
public RoiSet angleROItoXML(ArrayList<AngleROI> shapes,
                            RoiSet roiSetJAXB)
```
    Converts the ArrayList of AngleROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - polygonROItoXML
```
public RoiSet polygonROItoXML(ArrayList<PolygonROI> shapes,
                              RoiSet roiSetJAXB)
```
    Converts the ArrayList of PolygonROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - freehandROItoXML
```
public RoiSet freehandROItoXML(ArrayList<FreehandROI> shapes,
                               RoiSet roiSetJAXB)
```
    Converts the ArrayList of FreehandROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - ellipseROItoXML
```
public RoiSet ellipseROItoXML(ArrayList<EllipseROI> shapes,
                              RoiSet roiSetJAXB)
```
    Converts the ArrayList of EllipseROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - rectangleROItoXML
```
public RoiSet rectangleROItoXML(ArrayList<RectangleROI> shapes,
                                RoiSet roiSetJAXB)
```
    Converts the ArrayList of RectangleROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - pointROItoXML
```
public RoiSet pointROItoXML(ArrayList<PointROI> shapes,
                            RoiSet roiSetJAXB)
```
    Converts the ArrayList of PointROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - lineROItoXML
```
public RoiSet lineROItoXML(ArrayList<LineROI> shapes,
                           RoiSet roiSetJAXB)
```
    Converts the ArrayList of LineROIs to XML representation.
    
    Parameters:
    
    shapes -
    
    roiSetJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - toXML
```
public Data toXML(Object javaObject,
                  Data dataJAXB)
```
  - toXML
```
public Path toXML(PathIterator iter,
                  Path pathJAXB)
```
    Generates an XML representation of the given PathIterator object.
    
    Parameters:
    
    iter -
    
    pathJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - toXML
```
public Bounds toXML(Rectangle2D bounds,
                    Bounds boundsJAXB)
```
    Converts the boundaries from a Rectangle2D to the XML representation.
    
    Parameters:
    
    bounds -
    
    boundsJAXB - an existing object, if null, a new object will be generated
    
    Returns:
    
    the XML representation
  - toXML
```
public Point toXML(Point2D point,
                   Point pointJAXB,
                   String id)
```
    Converts a Point2D to the XML representation.
    
    Parameters:
    
    point -
    
    pointJAXB - an existing object, if null, a new object will be generated
    
    id -
    
    Returns:
    
    the XML representation
  - toXML
```
public Stroke toXML(BasicStroke stroke,
                    Stroke strokeJAXB,
                    String name)
```
    Converts a given BasicStroke instance to the serializable form.
    
    Parameters:
    
    stroke -
    
    strokeJAXB - an existing object, if null, a new object will be generated
    
    name -
    
    Returns:
    
    the XML representation
  - toXML
```
public Color toXML(Color c,
                   Color colorJAXB,
                   String name)
```
    Converts a given Color instance to the serializable form.
    
    Parameters:
    
    c -
    
    colorJAXB - an existing object, if null, a new object will be generated
    
    name -
    
    Returns:
    
    the assembled XML object
  - testLoad
```
private static void testLoad(File f)
```
  - main
```
public static void main(String[] args)
                 throws IOException,
                        ClassNotFoundException,
                        InterruptedException,
                        InstantiationException,
                        IllegalAccessException
```
    Throws:
    
    IOException
    
    ClassNotFoundException
    
    InterruptedException
    
    InstantiationException
    
    IllegalAccessException

Class XMLAnnotationManager

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

logger

xmlSchemaLocation

XML_DATA_ENCODING

xmlFile

xmlSchemaFileIS

allLayers

jaxbContext

marshaller

unmarshaller

allLayersJAXB

of

Constructor Detail

XMLAnnotationManager

XMLAnnotationManager

Method Detail

getXmlFile

setXmlFile

setAllLayers

getAllLayers

validate

writeXML

write

read

readXML

convertToList

parseXMLPointROI

parseXMLRectangleROI

parseXMLAngleROI

parseXMLEllipseROI

parseXMLFreehandROI

parseXMLLineROI

parseXMLPolygonROI

parseXML

parseXML

parseXML

parseXML

convertToXML

angleROItoXML

polygonROItoXML

freehandROItoXML

ellipseROItoXML

rectangleROItoXML

pointROItoXML

lineROItoXML

toXML

toXML

toXML

toXML

toXML

toXML

testLoad

main