ome.xml.model

Class Plate

java.lang.Object

ome.xml.model.AbstractOMEModelObject

ome.xml.model.Plate

All Implemented Interfaces:

OMEModelObject

public class Plate
extends AbstractOMEModelObject

Field Summary

Fields

Modifier and Type	Field and Description
static String	NAMESPACE

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	addPlateAcquisition(PlateAcquisition plateAcquisition)
void	addWell(Well well)
Element	asXMLElement(Document document) Takes the entire object hierarchy and produces an XML DOM tree.
protected Element	asXMLElement(Document document, Element Plate_element) Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
List<Annotation>	copyLinkedAnnotationList()
List<Screen>	copyLinkedScreenList()
List<PlateAcquisition>	copyPlateAcquisitionList()
List<Well>	copyWellList()
NamingConvention	getColumnNamingConvention()
PositiveInteger	getColumns()
String	getDescription()
String	getExternalIdentifier()
NonNegativeInteger	getFieldIndex()
String	getID()
Annotation	getLinkedAnnotation(int index)
Screen	getLinkedScreen(int index)
String	getName()
PlateAcquisition	getPlateAcquisition(int index)
NamingConvention	getRowNamingConvention()
PositiveInteger	getRows()
String	getStatus()
Well	getWell(int index)
Double	getWellOriginX()
Double	getWellOriginY()
boolean	link(Reference reference, OMEModelObject o) Link a given OME model object to this model object.
boolean	linkAnnotation(Annotation o)
boolean	linkScreen(Screen o)
void	removePlateAcquisition(PlateAcquisition plateAcquisition)
void	removeWell(Well well)
void	setColumnNamingConvention(NamingConvention columnNamingConvention)
void	setColumns(PositiveInteger columns)
void	setDescription(String description)
void	setExternalIdentifier(String externalIdentifier)
void	setFieldIndex(NonNegativeInteger fieldIndex)
void	setID(String id)
Annotation	setLinkedAnnotation(int index, Annotation o)
Screen	setLinkedScreen(int index, Screen o)
void	setName(String name)
PlateAcquisition	setPlateAcquisition(int index, PlateAcquisition plateAcquisition)
void	setRowNamingConvention(NamingConvention rowNamingConvention)
void	setRows(PositiveInteger rows)
void	setStatus(String status)
Well	setWell(int index, Well well)
void	setWellOriginX(Double wellOriginX)
void	setWellOriginY(Double wellOriginY)
int	sizeOfLinkedAnnotationList()
int	sizeOfLinkedScreenList()
int	sizeOfPlateAcquisitionList()
int	sizeOfWellList()
boolean	unlinkAnnotation(Annotation o)
boolean	unlinkScreen(Screen o)
void	update(Element element, OMEModel model) Updates Plate recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject

getChildrenByTagName, stripNamespacePrefix, update

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

Constructor Detail

Plate

public Plate()

Default constructor.

Plate

public Plate(Element element,
     OMEModel model)
      throws EnumerationException

Constructs Plate 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.

Method Detail

update

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

Updates Plate 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.

getStatus

public String getStatus()

setStatus

public void setStatus(String status)

getRows

public PositiveInteger getRows()

setRows

public void setRows(PositiveInteger rows)

getExternalIdentifier

public String getExternalIdentifier()

setExternalIdentifier

public void setExternalIdentifier(String externalIdentifier)

getRowNamingConvention

public NamingConvention getRowNamingConvention()

setRowNamingConvention

public void setRowNamingConvention(NamingConvention rowNamingConvention)

getColumnNamingConvention

public NamingConvention getColumnNamingConvention()

setColumnNamingConvention

public void setColumnNamingConvention(NamingConvention columnNamingConvention)

getFieldIndex

public NonNegativeInteger getFieldIndex()

setFieldIndex

public void setFieldIndex(NonNegativeInteger fieldIndex)

getWellOriginY

public Double getWellOriginY()

setWellOriginY

public void setWellOriginY(Double wellOriginY)

getWellOriginX

public Double getWellOriginX()

setWellOriginX

public void setWellOriginX(Double wellOriginX)

getID

public String getID()

setID

public void setID(String id)

getColumns

public PositiveInteger getColumns()

setColumns

public void setColumns(PositiveInteger columns)

getName

public String getName()

setName

public void setName(String name)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

sizeOfWellList

public int sizeOfWellList()

copyWellList

public List<Well> copyWellList()

getWell

public Well getWell(int index)

setWell

public Well setWell(int index,
           Well well)

addWell

public void addWell(Well well)

removeWell

public void removeWell(Well well)

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)

sizeOfPlateAcquisitionList

public int sizeOfPlateAcquisitionList()

copyPlateAcquisitionList

public List<PlateAcquisition> copyPlateAcquisitionList()

getPlateAcquisition

public PlateAcquisition getPlateAcquisition(int index)

setPlateAcquisition

public PlateAcquisition setPlateAcquisition(int index,
                                   PlateAcquisition plateAcquisition)

addPlateAcquisition

public void addPlateAcquisition(PlateAcquisition plateAcquisition)

removePlateAcquisition

public void removePlateAcquisition(PlateAcquisition plateAcquisition)

sizeOfLinkedScreenList

public int sizeOfLinkedScreenList()

copyLinkedScreenList

public List<Screen> copyLinkedScreenList()

getLinkedScreen

public Screen getLinkedScreen(int index)

setLinkedScreen

public Screen setLinkedScreen(int index,
                     Screen o)

linkScreen

public boolean linkScreen(Screen o)

unlinkScreen

public boolean unlinkScreen(Screen 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 Plate_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.

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

Returns:

element populated with properties from this class.