ome.xml.model

Class Well

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Well

All Implemented Interfaces:

OMEModelObject

public class Well
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	NAMESPACE

Constructor Summary

Constructors

Constructor and Description
Well() Default constructor.
Well(org.w3c.dom.Element element, OMEModel model) Constructs Well recursively from an XML DOM tree.
Well(Well orig) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addWellSample(WellSample wellSample)
org.w3c.dom.Element	asXMLElement(org.w3c.dom.Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected org.w3c.dom.Element	asXMLElement(org.w3c.dom.Document document, org.w3c.dom.Element Well_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
java.util.List<Annotation>	copyLinkedAnnotationList()
java.util.List<WellSample>	copyWellSampleList()
Color	getColor()
NonNegativeInteger	getColumn()
java.lang.String	getExternalDescription()
java.lang.String	getExternalIdentifier()
java.lang.String	getID()
Annotation	getLinkedAnnotation(int index)
Reagent	getLinkedReagent()
Plate	getPlate()
NonNegativeInteger	getRow()
java.lang.String	getType()
WellSample	getWellSample(int index)
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
void	linkReagent(Reagent o)
void	removeWellSample(WellSample wellSample)
void	setColor(Color color)
void	setColumn(NonNegativeInteger column)
void	setExternalDescription(java.lang.String externalDescription)
void	setExternalIdentifier(java.lang.String externalIdentifier)
void	setID(java.lang.String id)
Annotation	setLinkedAnnotation(int index, Annotation o)
void	setPlate(Plate plate_BackReference)
void	setRow(NonNegativeInteger row)
void	setType(java.lang.String type)
WellSample	setWellSample(int index, WellSample wellSample)
int	sizeOfLinkedAnnotationList()
int	sizeOfWellSampleList()
boolean	unlinkAnnotation(Annotation o)
void	unlinkReagent(Reagent o)
void	update(org.w3c.dom.Element element, OMEModel model) Updates Well 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 java.lang.String NAMESPACE

See Also:

Constant Field Values

Constructor Detail

Well

public Well()

Default constructor.

Well

public Well(org.w3c.dom.Element element,
    OMEModel model)
     throws EnumerationException

Constructs Well 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.

Well

public Well(Well orig)

Copy constructor.

Method Detail

update

public void update(org.w3c.dom.Element element,
          OMEModel model)
            throws EnumerationException

Updates Well 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.

getExternalIdentifier

public java.lang.String getExternalIdentifier()

setExternalIdentifier

public void setExternalIdentifier(java.lang.String externalIdentifier)

getColumn

public NonNegativeInteger getColumn()

setColumn

public void setColumn(NonNegativeInteger column)

getExternalDescription

public java.lang.String getExternalDescription()

setExternalDescription

public void setExternalDescription(java.lang.String externalDescription)

getColor

public Color getColor()

setColor

public void setColor(Color color)

getType

public java.lang.String getType()

setType

public void setType(java.lang.String type)

getID

public java.lang.String getID()

setID

public void setID(java.lang.String id)

getRow

public NonNegativeInteger getRow()

setRow

public void setRow(NonNegativeInteger row)

sizeOfWellSampleList

public int sizeOfWellSampleList()

copyWellSampleList

public java.util.List<WellSample> copyWellSampleList()

getWellSample

public WellSample getWellSample(int index)

setWellSample

public WellSample setWellSample(int index,
                       WellSample wellSample)

addWellSample

public void addWellSample(WellSample wellSample)

removeWellSample

public void removeWellSample(WellSample wellSample)

getLinkedReagent

public Reagent getLinkedReagent()

linkReagent

public void linkReagent(Reagent o)

unlinkReagent

public void unlinkReagent(Reagent o)

sizeOfLinkedAnnotationList

public int sizeOfLinkedAnnotationList()

copyLinkedAnnotationList

public java.util.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)

getPlate

public Plate getPlate()

setPlate

public void setPlate(Plate plate_BackReference)

asXMLElement

public org.w3c.dom.Element asXMLElement(org.w3c.dom.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 org.w3c.dom.Element asXMLElement(org.w3c.dom.Document document,
                               org.w3c.dom.Element Well_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.

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

Returns:

element populated with properties from this class.