Plate (Bio-Formats API)

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
`private List<Annotation>`	`annotationLinks`
`private NamingConvention`	`columnNamingConvention`
`private PositiveInteger`	`columns`
`private String`	`description`
`private String`	`externalIdentifier`
`private NonNegativeInteger`	`fieldIndex`
`private String`	`id`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`private String`	`name`
`static String`	`NAMESPACE`
`private List<PlateAcquisition>`	`plateAcquisitions`
`private NamingConvention`	`rowNamingConvention`
`private PositiveInteger`	`rows`
`private List<Screen>`	`screenLinks`
`private String`	`status`
`private Length`	`wellOriginX`
`private Length`	`wellOriginY`
`private List<Well>`	`wells`

Constructor Summary

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

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)`
`Length`	`getWellOriginX()`
`static String`	`getWellOriginXUnitXsdDefault()`
`Length`	`getWellOriginY()`
`static String`	`getWellOriginYUnitXsdDefault()`
`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(Length wellOriginX)`
`void`	`setWellOriginY(Length 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

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.

status
```
private String status
```

rows
```
private PositiveInteger rows
```

externalIdentifier
```
private String externalIdentifier
```

rowNamingConvention

private NamingConvention rowNamingConvention

columnNamingConvention

private NamingConvention columnNamingConvention

fieldIndex
```
private NonNegativeInteger fieldIndex
```

columns
```
private PositiveInteger columns
```

wellOriginY
```
private Length wellOriginY
```

wellOriginX
```
private Length wellOriginX
```

id
```
private String id
```

name
```
private String name
```

description
```
private String description
```

wells
```
private List<Well> wells
```

annotationLinks

private List<Annotation> annotationLinks

plateAcquisitions

private List<PlateAcquisition> plateAcquisitions

screenLinks
```
private List<Screen> screenLinks
```

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.
- Plate
```
public Plate(Plate orig)
```
  Copy constructor.

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)

getWellOriginXUnitXsdDefault

public static String getWellOriginXUnitXsdDefault()

getColumnNamingConvention

public NamingConvention getColumnNamingConvention()

setColumnNamingConvention

public void setColumnNamingConvention(NamingConvention columnNamingConvention)

getFieldIndex

public NonNegativeInteger getFieldIndex()

setFieldIndex

public void setFieldIndex(NonNegativeInteger fieldIndex)

getColumns
```
public PositiveInteger getColumns()
```

setColumns

public void setColumns(PositiveInteger columns)

getWellOriginY
```
public Length getWellOriginY()
```

setWellOriginY

public void setWellOriginY(Length wellOriginY)

getWellOriginX
```
public Length getWellOriginX()
```

setWellOriginX

public void setWellOriginX(Length wellOriginX)

getID
```
public String getID()
```

setID
```
public void setID(String id)
```

getWellOriginYUnitXsdDefault

public static String getWellOriginYUnitXsdDefault()

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.

Class Plate

Field Summary

Constructor Summary

Method Summary

Methods inherited from class ome.xml.model.AbstractOMEModelObject

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

LOGGER

status

rows

externalIdentifier

rowNamingConvention

columnNamingConvention

fieldIndex

columns

wellOriginY

wellOriginX

id

name

description

wells

annotationLinks

plateAcquisitions

screenLinks

Constructor Detail

Plate

Plate

Plate

Method Detail

update

link

getStatus

setStatus

getRows

setRows

getExternalIdentifier

setExternalIdentifier

getRowNamingConvention

setRowNamingConvention

getWellOriginXUnitXsdDefault

getColumnNamingConvention

setColumnNamingConvention

getFieldIndex

setFieldIndex

getColumns

setColumns

getWellOriginY

setWellOriginY

getWellOriginX

setWellOriginX

getID

setID

getWellOriginYUnitXsdDefault

getName

setName

getDescription

setDescription

sizeOfWellList

copyWellList

getWell

setWell

addWell

removeWell

sizeOfLinkedAnnotationList

copyLinkedAnnotationList

getLinkedAnnotation

setLinkedAnnotation

linkAnnotation

unlinkAnnotation

sizeOfPlateAcquisitionList

copyPlateAcquisitionList

getPlateAcquisition

setPlateAcquisition

addPlateAcquisition

removePlateAcquisition

sizeOfLinkedScreenList

copyLinkedScreenList

getLinkedScreen

setLinkedScreen