ome.xml.model

Class Instrument

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Instrument

All Implemented Interfaces:

OMEModelObject

public class Instrument
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
private List<Annotation>	annotationLinks
private List<Detector>	detectors
private List<Dichroic>	dichroics
private List<Filter>	filters
private List<FilterSet>	filterSets
private String	id
private List<Image>	images
private List<LightSource>	lightSources
private static org.slf4j.Logger	LOGGER Logger for this class.
private Microscope	microscope
static String	NAMESPACE
private List<Objective>	objectives

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	addDetector(Detector detector)
void	addDichroic(Dichroic dichroic)
void	addFilter(Filter filter)
void	addFilterSet(FilterSet filterSet)
void	addLightSource(LightSource lightSource)
void	addObjective(Objective objective)
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Instrument_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<Detector>	copyDetectorList()
List<Dichroic>	copyDichroicList()
List<Filter>	copyFilterList()
List<FilterSet>	copyFilterSetList()
List<LightSource>	copyLightSourceList()
List<Annotation>	copyLinkedAnnotationList()
List<Image>	copyLinkedImageList()
List<Objective>	copyObjectiveList()
Detector	getDetector(int index)
Dichroic	getDichroic(int index)
Filter	getFilter(int index)
FilterSet	getFilterSet(int index)
String	getID()
LightSource	getLightSource(int index)
Annotation	getLinkedAnnotation(int index)
Image	getLinkedImage(int index)
Microscope	getMicroscope()
Objective	getObjective(int index)
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
boolean	linkImage(Image o)
void	removeDetector(Detector detector)
void	removeDichroic(Dichroic dichroic)
void	removeFilter(Filter filter)
void	removeFilterSet(FilterSet filterSet)
void	removeLightSource(LightSource lightSource)
void	removeObjective(Objective objective)
Detector	setDetector(int index, Detector detector)
Dichroic	setDichroic(int index, Dichroic dichroic)
Filter	setFilter(int index, Filter filter)
FilterSet	setFilterSet(int index, FilterSet filterSet)
void	setID(String id)
LightSource	setLightSource(int index, LightSource lightSource)
Annotation	setLinkedAnnotation(int index, Annotation o)
Image	setLinkedImage(int index, Image o)
void	setMicroscope(Microscope microscope)
Objective	setObjective(int index, Objective objective)
int	sizeOfDetectorList()
int	sizeOfDichroicList()
int	sizeOfFilterList()
int	sizeOfFilterSetList()
int	sizeOfLightSourceList()
int	sizeOfLinkedAnnotationList()
int	sizeOfLinkedImageList()
int	sizeOfObjectiveList()
boolean	unlinkAnnotation(Annotation o)
boolean	unlinkImage(Image o)
void	update(Element element, OMEModel model) Updates Instrument 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.

id

private String id

microscope

private Microscope microscope

lightSources

private List<LightSource> lightSources

detectors

private List<Detector> detectors

objectives

private List<Objective> objectives

filterSets

private List<FilterSet> filterSets

filters

private List<Filter> filters

dichroics

private List<Dichroic> dichroics

annotationLinks

private List<Annotation> annotationLinks

images

private List<Image> images

Constructor Detail

Instrument

public Instrument()

Default constructor.

Instrument

public Instrument(Element element,
          OMEModel model)
           throws EnumerationException

Constructs Instrument 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.

Instrument

public Instrument(Instrument orig)

Copy constructor.

Method Detail

update

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

Updates Instrument 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.

getID

public String getID()

setID

public void setID(String id)

getMicroscope

public Microscope getMicroscope()

setMicroscope

public void setMicroscope(Microscope microscope)

sizeOfLightSourceList

public int sizeOfLightSourceList()

copyLightSourceList

public List<LightSource> copyLightSourceList()

getLightSource

public LightSource getLightSource(int index)

setLightSource

public LightSource setLightSource(int index,
                         LightSource lightSource)

addLightSource

public void addLightSource(LightSource lightSource)

removeLightSource

public void removeLightSource(LightSource lightSource)

sizeOfDetectorList

public int sizeOfDetectorList()

copyDetectorList

public List<Detector> copyDetectorList()

getDetector

public Detector getDetector(int index)

setDetector

public Detector setDetector(int index,
                   Detector detector)

addDetector

public void addDetector(Detector detector)

removeDetector

public void removeDetector(Detector detector)

sizeOfObjectiveList

public int sizeOfObjectiveList()

copyObjectiveList

public List<Objective> copyObjectiveList()

getObjective

public Objective getObjective(int index)

setObjective

public Objective setObjective(int index,
                     Objective objective)

addObjective

public void addObjective(Objective objective)

removeObjective

public void removeObjective(Objective objective)

sizeOfFilterSetList

public int sizeOfFilterSetList()

copyFilterSetList

public List<FilterSet> copyFilterSetList()

getFilterSet

public FilterSet getFilterSet(int index)

setFilterSet

public FilterSet setFilterSet(int index,
                     FilterSet filterSet)

addFilterSet

public void addFilterSet(FilterSet filterSet)

removeFilterSet

public void removeFilterSet(FilterSet filterSet)

sizeOfFilterList

public int sizeOfFilterList()

copyFilterList

public List<Filter> copyFilterList()

getFilter

public Filter getFilter(int index)

setFilter

public Filter setFilter(int index,
               Filter filter)

addFilter

public void addFilter(Filter filter)

removeFilter

public void removeFilter(Filter filter)

sizeOfDichroicList

public int sizeOfDichroicList()

copyDichroicList

public List<Dichroic> copyDichroicList()

getDichroic

public Dichroic getDichroic(int index)

setDichroic

public Dichroic setDichroic(int index,
                   Dichroic dichroic)

addDichroic

public void addDichroic(Dichroic dichroic)

removeDichroic

public void removeDichroic(Dichroic dichroic)

sizeOfLinkedAnnotationList

public int sizeOfLinkedAnnotationList()

copyLinkedAnnotationList

public List<Annotation> copyLinkedAnnotationList()

getLinkedAnnotation

public Annotation getLinkedAnnotation(int index)

setLinkedAnnotation

public Annotation setLinkedAnnotation(int index,
                             Annotation o)

linkAnnotation

public boolean linkAnnotation(Annotation o)

unlinkAnnotation

public boolean unlinkAnnotation(Annotation o)

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 Instrument_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.

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

Returns:

element populated with properties from this class.