ome.xml.model

Class Experiment

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Experiment

All Implemented Interfaces:

OMEModelObject

public class Experiment
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
private String	description
private Experimenter	experimenter
private String	id
private List<Image>	images
private static org.slf4j.Logger	LOGGER Logger for this class.
private List<MicrobeamManipulation>	microbeamManipulations
static String	NAMESPACE
private ExperimentType	type

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	addMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Experiment_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<Image>	copyLinkedImageList()
List<MicrobeamManipulation>	copyMicrobeamManipulationList()
String	getDescription()
String	getID()
Experimenter	getLinkedExperimenter()
Image	getLinkedImage(int index)
MicrobeamManipulation	getMicrobeamManipulation(int index)
ExperimentType	getType()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
void	linkExperimenter(Experimenter o)
boolean	linkImage(Image o)
void	removeMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
void	setDescription(String description)
void	setID(String id)
Image	setLinkedImage(int index, Image o)
MicrobeamManipulation	setMicrobeamManipulation(int index, MicrobeamManipulation microbeamManipulation)
void	setType(ExperimentType type)
int	sizeOfLinkedImageList()
int	sizeOfMicrobeamManipulationList()
void	unlinkExperimenter(Experimenter o)
boolean	unlinkImage(Image o)
void	update(Element element, OMEModel model) Updates Experiment 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.

type

private ExperimentType type

id

private String id

description

private String description

experimenter

private Experimenter experimenter

microbeamManipulations

private List<MicrobeamManipulation> microbeamManipulations

images

private List<Image> images

Constructor Detail

Experiment

public Experiment()

Default constructor.

Experiment

public Experiment(Element element,
          OMEModel model)
           throws EnumerationException

Constructs Experiment 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.

Experiment

public Experiment(Experiment orig)

Copy constructor.

Method Detail

update

public void update(Element element,
          OMEModel model)
            throws EnumerationException

Updates Experiment 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.

getType

public ExperimentType getType()

setType

public void setType(ExperimentType type)

getID

public String getID()

setID

public void setID(String id)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getLinkedExperimenter

public Experimenter getLinkedExperimenter()

linkExperimenter

public void linkExperimenter(Experimenter o)

unlinkExperimenter

public void unlinkExperimenter(Experimenter o)

sizeOfMicrobeamManipulationList

public int sizeOfMicrobeamManipulationList()

copyMicrobeamManipulationList

public List<MicrobeamManipulation> copyMicrobeamManipulationList()

getMicrobeamManipulation

public MicrobeamManipulation getMicrobeamManipulation(int index)

setMicrobeamManipulation

public MicrobeamManipulation setMicrobeamManipulation(int index,
                                             MicrobeamManipulation microbeamManipulation)

addMicrobeamManipulation

public void addMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)

removeMicrobeamManipulation

public void removeMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)

sizeOfLinkedImageList

public int sizeOfLinkedImageList()

copyLinkedImageList

public List<Image> copyLinkedImageList()

getLinkedImage

public Image getLinkedImage(int index)

setLinkedImage

public Image setLinkedImage(int index,
                   Image o)

linkImage

public boolean linkImage(Image o)

unlinkImage

public boolean unlinkImage(Image o)

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 Experiment_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.

Experiment_element - Element from the subclass. If null a new element will be created of this class.

Returns:

element populated with properties from this class.