OME (Bio-Formats API)

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

All Implemented Interfaces:

OMEModelObject

Direct Known Subclasses:

OMEXMLMetadataRoot
```
public class OME
extends AbstractOMEModelObject
```

Field Summary

Fields
Modifier and Type	Field and Description
`private BinaryOnly`	`binaryOnly`
`private String`	`creator`
`private List<Dataset>`	`datasets`
`private List<ExperimenterGroup>`	`experimenterGroups`
`private List<Experimenter>`	`experimenters`
`private List<Experiment>`	`experiments`
`private List<Image>`	`images`
`private List<Instrument>`	`instruments`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`static String`	`NAMESPACE`
`private List<Plate>`	`plates`
`private List<Project>`	`projects`
`private Rights`	`rights`
`private List<ROI>`	`roIs`
`private List<Screen>`	`screens`
`private StructuredAnnotations`	`structuredAnnotations`
`private String`	`uuid`

Constructor Summary

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addDataset(Dataset dataset)`
`void`	`addExperiment(Experiment experiment)`
`void`	`addExperimenter(Experimenter experimenter)`
`void`	`addExperimenterGroup(ExperimenterGroup experimenterGroup)`
`void`	`addImage(Image image)`
`void`	`addInstrument(Instrument instrument)`
`void`	`addPlate(Plate plate)`
`void`	`addProject(Project project)`
`void`	`addROI(ROI roi)`
`void`	`addScreen(Screen screen)`
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element OME_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<Dataset>`	`copyDatasetList()`
`List<ExperimenterGroup>`	`copyExperimenterGroupList()`
`List<Experimenter>`	`copyExperimenterList()`
`List<Experiment>`	`copyExperimentList()`
`List<Image>`	`copyImageList()`
`List<Instrument>`	`copyInstrumentList()`
`List<Plate>`	`copyPlateList()`
`List<Project>`	`copyProjectList()`
`List<ROI>`	`copyROIList()`
`List<Screen>`	`copyScreenList()`
`BinaryOnly`	`getBinaryOnly()`
`String`	`getCreator()`
`Dataset`	`getDataset(int index)`
`Experiment`	`getExperiment(int index)`
`Experimenter`	`getExperimenter(int index)`
`ExperimenterGroup`	`getExperimenterGroup(int index)`
`Image`	`getImage(int index)`
`Instrument`	`getInstrument(int index)`
`Plate`	`getPlate(int index)`
`Project`	`getProject(int index)`
`Rights`	`getRights()`
`ROI`	`getROI(int index)`
`Screen`	`getScreen(int index)`
`StructuredAnnotations`	`getStructuredAnnotations()`
`String`	`getUUID()`
`boolean`	`link(Reference reference, OMEModelObject o)` Link a given OME model object to this model object.
`void`	`removeDataset(Dataset dataset)`
`void`	`removeExperiment(Experiment experiment)`
`void`	`removeExperimenter(Experimenter experimenter)`
`void`	`removeExperimenterGroup(ExperimenterGroup experimenterGroup)`
`void`	`removeImage(Image image)`
`void`	`removeInstrument(Instrument instrument)`
`void`	`removePlate(Plate plate)`
`void`	`removeProject(Project project)`
`void`	`removeROI(ROI roi)`
`void`	`removeScreen(Screen screen)`
`void`	`setBinaryOnly(BinaryOnly binaryOnly)`
`void`	`setCreator(String creator)`
`Dataset`	`setDataset(int index, Dataset dataset)`
`Experiment`	`setExperiment(int index, Experiment experiment)`
`Experimenter`	`setExperimenter(int index, Experimenter experimenter)`
`ExperimenterGroup`	`setExperimenterGroup(int index, ExperimenterGroup experimenterGroup)`
`Image`	`setImage(int index, Image image)`
`Instrument`	`setInstrument(int index, Instrument instrument)`
`Plate`	`setPlate(int index, Plate plate)`
`Project`	`setProject(int index, Project project)`
`void`	`setRights(Rights rights)`
`ROI`	`setROI(int index, ROI roi)`
`Screen`	`setScreen(int index, Screen screen)`
`void`	`setStructuredAnnotations(StructuredAnnotations structuredAnnotations)`
`void`	`setUUID(String uuid)`
`int`	`sizeOfDatasetList()`
`int`	`sizeOfExperimenterGroupList()`
`int`	`sizeOfExperimenterList()`
`int`	`sizeOfExperimentList()`
`int`	`sizeOfImageList()`
`int`	`sizeOfInstrumentList()`
`int`	`sizeOfPlateList()`
`int`	`sizeOfProjectList()`
`int`	`sizeOfROIList()`
`int`	`sizeOfScreenList()`
`void`	`update(Element element, OMEModel model)` Updates OME 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.

uuid
```
private String uuid
```

creator
```
private String creator
```

rights
```
private Rights rights
```

projects
```
private List<Project> projects
```

datasets
```
private List<Dataset> datasets
```

experiments
```
private List<Experiment> experiments
```

plates
```
private List<Plate> plates
```

screens
```
private List<Screen> screens
```

experimenters

private List<Experimenter> experimenters

experimenterGroups

private List<ExperimenterGroup> experimenterGroups

instruments
```
private List<Instrument> instruments
```

images
```
private List<Image> images
```

structuredAnnotations

private StructuredAnnotations structuredAnnotations

roIs
```
private List<ROI> roIs
```

binaryOnly
```
private BinaryOnly binaryOnly
```

Constructor Detail
- OME
```
public OME()
```
  Default constructor.
- OME
```
public OME(Element element,
   OMEModel model)
    throws EnumerationException
```
  Constructs OME 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.
- OME
```
public OME(OME orig)
```
  Copy constructor.

Method Detail

update
```
public void update(Element element,
          OMEModel model)
            throws EnumerationException
```
Updates OME 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.

getUUID
```
public String getUUID()
```

setUUID
```
public void setUUID(String uuid)
```

getCreator
```
public String getCreator()
```

setCreator

public void setCreator(String creator)

getRights
```
public Rights getRights()
```

setRights
```
public void setRights(Rights rights)
```

sizeOfProjectList
```
public int sizeOfProjectList()
```

copyProjectList

public List<Project> copyProjectList()

getProject
```
public Project getProject(int index)
```

setProject

public Project setProject(int index,
                 Project project)

addProject

public void addProject(Project project)

removeProject

public void removeProject(Project project)

sizeOfDatasetList
```
public int sizeOfDatasetList()
```

copyDatasetList

public List<Dataset> copyDatasetList()

getDataset
```
public Dataset getDataset(int index)
```

setDataset

public Dataset setDataset(int index,
                 Dataset dataset)

addDataset

public void addDataset(Dataset dataset)

removeDataset

public void removeDataset(Dataset dataset)

sizeOfExperimentList
```
public int sizeOfExperimentList()
```

copyExperimentList

public List<Experiment> copyExperimentList()

getExperiment

public Experiment getExperiment(int index)

setExperiment

public Experiment setExperiment(int index,
                       Experiment experiment)

addExperiment

public void addExperiment(Experiment experiment)

removeExperiment

public void removeExperiment(Experiment experiment)

sizeOfPlateList
```
public int sizeOfPlateList()
```

copyPlateList
```
public List<Plate> copyPlateList()
```

getPlate
```
public Plate getPlate(int index)
```

setPlate

public Plate setPlate(int index,
             Plate plate)

addPlate
```
public void addPlate(Plate plate)
```

removePlate
```
public void removePlate(Plate plate)
```

sizeOfScreenList
```
public int sizeOfScreenList()
```

copyScreenList
```
public List<Screen> copyScreenList()
```

getScreen
```
public Screen getScreen(int index)
```

setScreen

public Screen setScreen(int index,
               Screen screen)

addScreen
```
public void addScreen(Screen screen)
```

removeScreen

public void removeScreen(Screen screen)

sizeOfExperimenterList
```
public int sizeOfExperimenterList()
```

copyExperimenterList

public List<Experimenter> copyExperimenterList()

getExperimenter

public Experimenter getExperimenter(int index)

setExperimenter

public Experimenter setExperimenter(int index,
                           Experimenter experimenter)

addExperimenter

public void addExperimenter(Experimenter experimenter)

removeExperimenter

public void removeExperimenter(Experimenter experimenter)

sizeOfExperimenterGroupList

public int sizeOfExperimenterGroupList()

copyExperimenterGroupList

public List<ExperimenterGroup> copyExperimenterGroupList()

getExperimenterGroup

public ExperimenterGroup getExperimenterGroup(int index)

setExperimenterGroup

public ExperimenterGroup setExperimenterGroup(int index,
                                     ExperimenterGroup experimenterGroup)

addExperimenterGroup

public void addExperimenterGroup(ExperimenterGroup experimenterGroup)

removeExperimenterGroup

public void removeExperimenterGroup(ExperimenterGroup experimenterGroup)

sizeOfInstrumentList
```
public int sizeOfInstrumentList()
```

copyInstrumentList

public List<Instrument> copyInstrumentList()

getInstrument

public Instrument getInstrument(int index)

setInstrument

public Instrument setInstrument(int index,
                       Instrument instrument)

addInstrument

public void addInstrument(Instrument instrument)

removeInstrument

public void removeInstrument(Instrument instrument)

sizeOfImageList
```
public int sizeOfImageList()
```

copyImageList
```
public List<Image> copyImageList()
```

getImage
```
public Image getImage(int index)
```

setImage

public Image setImage(int index,
             Image image)

addImage
```
public void addImage(Image image)
```

removeImage
```
public void removeImage(Image image)
```

getStructuredAnnotations

public StructuredAnnotations getStructuredAnnotations()

setStructuredAnnotations

public void setStructuredAnnotations(StructuredAnnotations structuredAnnotations)

sizeOfROIList
```
public int sizeOfROIList()
```

copyROIList
```
public List<ROI> copyROIList()
```

getROI
```
public ROI getROI(int index)
```

setROI

public ROI setROI(int index,
         ROI roi)

addROI
```
public void addROI(ROI roi)
```

removeROI
```
public void removeROI(ROI roi)
```

getBinaryOnly
```
public BinaryOnly getBinaryOnly()
```

setBinaryOnly

public void setBinaryOnly(BinaryOnly binaryOnly)

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 OME_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.
OME_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 OME

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

uuid

creator

rights

projects

datasets

experiments

plates

screens

experimenters

experimenterGroups

instruments

images

structuredAnnotations

roIs

binaryOnly

Constructor Detail

OME

OME

OME

Method Detail

update

link

getUUID

setUUID

getCreator

setCreator

getRights

setRights

sizeOfProjectList

copyProjectList

getProject

setProject

addProject

removeProject

sizeOfDatasetList

copyDatasetList

getDataset

setDataset

addDataset

removeDataset

sizeOfExperimentList

copyExperimentList

getExperiment

setExperiment

addExperiment

removeExperiment

sizeOfPlateList

copyPlateList

getPlate

setPlate

addPlate

removePlate

sizeOfScreenList

copyScreenList

getScreen

setScreen

addScreen

removeScreen

sizeOfExperimenterList

copyExperimenterList

getExperimenter

setExperimenter

addExperimenter

removeExperimenter

sizeOfExperimenterGroupList

copyExperimenterGroupList

getExperimenterGroup

setExperimenterGroup

addExperimenterGroup

removeExperimenterGroup

sizeOfInstrumentList