MicrobeamManipulation (Bio-Formats API)

java.lang.Object
- ome.xml.model.AbstractOMEModelObject
- - ome.xml.model.MicrobeamManipulation

All Implemented Interfaces:: OMEModelObject

public class MicrobeamManipulation
extends AbstractOMEModelObject

Field Summary

Fields
Modifier and Type	Field and Description
`private String`	`description`
`private Experiment`	`experiment`
`private Experimenter`	`experimenter`
`private String`	`id`
`private List<Image>`	`imageLinks`
`private List<LightSourceSettings>`	`lightSourceSettingsCombinations`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`static String`	`NAMESPACE`
`private List<ROI>`	`roiLinks`
`private MicrobeamManipulationType`	`type`

Constructor Summary

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addLightSourceSettings(LightSourceSettings lightSourceSettings)`
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element MicrobeamManipulation_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<LightSourceSettings>`	`copyLightSourceSettingsList()`
`List<Image>`	`copyLinkedImageList()`
`List<ROI>`	`copyLinkedROIList()`
`String`	`getDescription()`
`Experiment`	`getExperiment()`
`String`	`getID()`
`LightSourceSettings`	`getLightSourceSettings(int index)`
`Experimenter`	`getLinkedExperimenter()`
`Image`	`getLinkedImage(int index)`
`ROI`	`getLinkedROI(int index)`
`MicrobeamManipulationType`	`getType()`
`boolean`	`link(Reference reference, OMEModelObject o)` Link a given OME model object to this model object.
`void`	`linkExperimenter(Experimenter o)`
`boolean`	`linkImage(Image o)`
`boolean`	`linkROI(ROI o)`
`void`	`removeLightSourceSettings(LightSourceSettings lightSourceSettings)`
`void`	`setDescription(String description)`
`void`	`setExperiment(Experiment experiment_BackReference)`
`void`	`setID(String id)`
`LightSourceSettings`	`setLightSourceSettings(int index, LightSourceSettings lightSourceSettings)`
`Image`	`setLinkedImage(int index, Image o)`
`ROI`	`setLinkedROI(int index, ROI o)`
`void`	`setType(MicrobeamManipulationType type)`
`int`	`sizeOfLightSourceSettingsList()`
`int`	`sizeOfLinkedImageList()`
`int`	`sizeOfLinkedROIList()`
`void`	`unlinkExperimenter(Experimenter o)`
`boolean`	`unlinkImage(Image o)`
`boolean`	`unlinkROI(ROI o)`
`void`	`update(Element element, OMEModel model)` Updates MicrobeamManipulation 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.
  - type
```
private MicrobeamManipulationType type
```
  - id
```
private String id
```
  - description
```
private String description
```
  - roiLinks
```
private List<ROI> roiLinks
```
  - experimenter
```
private Experimenter experimenter
```
  - lightSourceSettingsCombinations
```
private List<LightSourceSettings> lightSourceSettingsCombinations
```
  - imageLinks
```
private List<Image> imageLinks
```
  - experiment
```
private Experiment experiment
```
- Constructor Detail
  - MicrobeamManipulation
```
public MicrobeamManipulation()
```
    Default constructor.
  - MicrobeamManipulation
```
public MicrobeamManipulation(Element element,
                     OMEModel model)
                      throws EnumerationException
```
    Constructs MicrobeamManipulation 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.
  - MicrobeamManipulation
```
public MicrobeamManipulation(MicrobeamManipulation orig)
```
    Copy constructor.
- Method Detail
  - update
```
public void update(Element element,
          OMEModel model)
            throws EnumerationException
```
    Updates MicrobeamManipulation 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.
  - getType
```
public MicrobeamManipulationType getType()
```
  - setType
```
public void setType(MicrobeamManipulationType type)
```
  - getID
```
public String getID()
```
  - setID
```
public void setID(String id)
```
  - getDescription
```
public String getDescription()
```
  - setDescription
```
public void setDescription(String description)
```
  - sizeOfLinkedROIList
```
public int sizeOfLinkedROIList()
```
  - copyLinkedROIList
```
public List<ROI> copyLinkedROIList()
```
  - getLinkedROI
```
public ROI getLinkedROI(int index)
```
  - setLinkedROI
```
public ROI setLinkedROI(int index,
               ROI o)
```
  - linkROI
```
public boolean linkROI(ROI o)
```
  - unlinkROI
```
public boolean unlinkROI(ROI o)
```
  - getLinkedExperimenter
```
public Experimenter getLinkedExperimenter()
```
  - linkExperimenter
```
public void linkExperimenter(Experimenter o)
```
  - unlinkExperimenter
```
public void unlinkExperimenter(Experimenter o)
```
  - sizeOfLightSourceSettingsList
```
public int sizeOfLightSourceSettingsList()
```
  - copyLightSourceSettingsList
```
public List<LightSourceSettings> copyLightSourceSettingsList()
```
  - getLightSourceSettings
```
public LightSourceSettings getLightSourceSettings(int index)
```
  - setLightSourceSettings
```
public LightSourceSettings setLightSourceSettings(int index,
                                         LightSourceSettings lightSourceSettings)
```
  - addLightSourceSettings
```
public void addLightSourceSettings(LightSourceSettings lightSourceSettings)
```
  - removeLightSourceSettings
```
public void removeLightSourceSettings(LightSourceSettings lightSourceSettings)
```
  - 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)
```
  - getExperiment
```
public Experiment getExperiment()
```
  - setExperiment
```
public void setExperiment(Experiment experiment_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 MicrobeamManipulation_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.
    MicrobeamManipulation_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 MicrobeamManipulation

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

type

id

description

roiLinks

experimenter

lightSourceSettingsCombinations

imageLinks

experiment

Constructor Detail

MicrobeamManipulation

MicrobeamManipulation

MicrobeamManipulation

Method Detail

update

link

getType

setType

getID

setID

getDescription

setDescription

sizeOfLinkedROIList

copyLinkedROIList

getLinkedROI

setLinkedROI

linkROI

unlinkROI

getLinkedExperimenter

linkExperimenter

unlinkExperimenter

sizeOfLightSourceSettingsList

copyLightSourceSettingsList

getLightSourceSettings

setLightSourceSettings

addLightSourceSettings

removeLightSourceSettings

sizeOfLinkedImageList

copyLinkedImageList

getLinkedImage

setLinkedImage

linkImage

unlinkImage

getExperiment

setExperiment

asXMLElement

asXMLElement