Well (Bio-Formats API)

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
`private List<Annotation>`	`annotationLinks`
`private Color`	`color`
`private NonNegativeInteger`	`column`
`private String`	`externalDescription`
`private String`	`externalIdentifier`
`private String`	`id`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`static String`	`NAMESPACE`
`private Plate`	`plate`
`private Reagent`	`reagent`
`private NonNegativeInteger`	`row`
`private String`	`type`
`private List<WellSample>`	`wellSamples`

Constructor Summary

Constructors
Constructor and Description
`Well()` Default constructor.
`Well(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)`
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element Well_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<Annotation>`	`copyLinkedAnnotationList()`
`List<WellSample>`	`copyWellSampleList()`
`Color`	`getColor()`
`NonNegativeInteger`	`getColumn()`
`String`	`getExternalDescription()`
`String`	`getExternalIdentifier()`
`String`	`getID()`
`Annotation`	`getLinkedAnnotation(int index)`
`Reagent`	`getLinkedReagent()`
`Plate`	`getPlate()`
`NonNegativeInteger`	`getRow()`
`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(String externalDescription)`
`void`	`setExternalIdentifier(String externalIdentifier)`
`void`	`setID(String id)`
`Annotation`	`setLinkedAnnotation(int index, Annotation o)`
`void`	`setPlate(Plate plate_BackReference)`
`void`	`setRow(NonNegativeInteger row)`
`void`	`setType(String type)`
`WellSample`	`setWellSample(int index, WellSample wellSample)`
`int`	`sizeOfLinkedAnnotationList()`
`int`	`sizeOfWellSampleList()`
`boolean`	`unlinkAnnotation(Annotation o)`
`void`	`unlinkReagent(Reagent o)`
`void`	`update(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 String NAMESPACE
```
    See Also:
    Constant Field Values
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
    Logger for this class.
  - externalIdentifier
```
private String externalIdentifier
```
  - column
```
private NonNegativeInteger column
```
  - externalDescription
```
private String externalDescription
```
  - color
```
private Color color
```
  - type
```
private String type
```
  - id
```
private String id
```
  - row
```
private NonNegativeInteger row
```
  - wellSamples
```
private List<WellSample> wellSamples
```
  - reagent
```
private Reagent reagent
```
  - annotationLinks
```
private List<Annotation> annotationLinks
```
  - plate
```
private Plate plate
```
- Constructor Detail
  - Well
```
public Well()
```
    Default constructor.
  - Well
```
public Well(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(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 String getExternalIdentifier()
```
  - setExternalIdentifier
```
public void setExternalIdentifier(String externalIdentifier)
```
  - getColumn
```
public NonNegativeInteger getColumn()
```
  - setColumn
```
public void setColumn(NonNegativeInteger column)
```
  - getExternalDescription
```
public String getExternalDescription()
```
  - setExternalDescription
```
public void setExternalDescription(String externalDescription)
```
  - getColor
```
public Color getColor()
```
  - setColor
```
public void setColor(Color color)
```
  - getType
```
public String getType()
```
  - setType
```
public void setType(String type)
```
  - getID
```
public String getID()
```
  - setID
```
public void setID(String id)
```
  - getRow
```
public NonNegativeInteger getRow()
```
  - setRow
```
public void setRow(NonNegativeInteger row)
```
  - sizeOfWellSampleList
```
public int sizeOfWellSampleList()
```
  - copyWellSampleList
```
public 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 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 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 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.

Class Well

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

externalIdentifier

column

externalDescription

color

type

id

row

wellSamples

reagent

annotationLinks

plate

Constructor Detail

Well

Well

Well

Method Detail

update

link

getExternalIdentifier

setExternalIdentifier

getColumn

setColumn

getExternalDescription

setExternalDescription

getColor

setColor

getType

setType

getID

setID

getRow

setRow

sizeOfWellSampleList

copyWellSampleList

getWellSample

setWellSample

addWellSample

removeWellSample

getLinkedReagent

linkReagent

unlinkReagent

sizeOfLinkedAnnotationList

copyLinkedAnnotationList

getLinkedAnnotation

setLinkedAnnotation

linkAnnotation

unlinkAnnotation

getPlate

setPlate

asXMLElement

asXMLElement