Package fr.igred.omero.repository

Class PlateWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

fr.igred.omero.repository.GenericRepositoryObjectWrapper<PlateData>

fr.igred.omero.repository.PlateWrapper

public class PlateWrapper
extends GenericRepositoryObjectWrapper<PlateData>

Class containing a PlateData object.

Wraps function calls to the PlateData contained.

Nested Class Summary

Nested classes/interfaces inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

GenericRepositoryObjectWrapper.ReplacePolicy

Field Summary

Fields

Modifier and Type	Field	Description
static String	ANNOTATION_LINK	Annotation link name for this type of object

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

Constructor	Description
PlateWrapper(PlateData plate)	Constructor of the class PlateWrapper.

Method Summary

Modifier and Type	Method	Description
protected String	annotationLinkType()	Returns the type of annotation link for this object.
PlateData	asPlateData()	Deprecated. Returns the PlateData contained.
int	getColumnSequenceIndex()	Returns the index indicating how to label a column.
int	getDefaultSample()	Returns the currently selected field or 0.
String	getDescription()	Gets the plate description
String	getExternalIdentifier()	Returns the external identifier of the plate.
List<ImageWrapper>	getImages(Client client)	Returns the images contained in the wells of this plate.
String	getName()	Gets the plate name.
List<PlateAcquisitionWrapper>	getPlateAcquisitions()	Returns the plate acquisitions related to this plate.
String	getPlateType()	Returns the type of plate e.g.
int	getRowSequenceIndex()	Returns the index indicating how to label a row.
List<ScreenWrapper>	getScreens(Client client)	Retrieves the screens containing this plate.
String	getStatus()	Returns the status of the plate.
Length	getWellOriginX(omero.model.enums.UnitsLength unit)	Returns the x-coordinate in 2D-space of the well.
Length	getWellOriginY(omero.model.enums.UnitsLength unit)	Returns the y-coordinate in 2D-space of the well.
List<WellWrapper>	getWells(Client client)	Gets all wells in the plate available from OMERO.
void	refresh(Client client)	Reloads the plate from OMERO.
void	setDefaultSample(int value)	Sets the default sample.
void	setDescription(String description)	Sets the description of the plate.
void	setExternalIdentifier(String value)	Sets the external identifier.
void	setName(String name)	Sets the name of the plate.
void	setStatus(String value)	Sets the status.

Methods inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

copyAnnotationLinks, importImage, importImages

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addFileAnnotation, addKeyValuePair, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValue, isLinked, link, link, linkIfNotLinked, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, flatten, getCreated, getGroupId, getId, getOwner, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ANNOTATION_LINK

public static final String ANNOTATION_LINK

Annotation link name for this type of object

See Also:

Constant Field Values

Constructor Detail

PlateWrapper

public PlateWrapper(PlateData plate)

Constructor of the class PlateWrapper.

Parameters:

plate - The plate contained in the PlateWrapper.

Method Detail

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<PlateData>

Returns:

See above.

getName

public String getName()

Gets the plate name.

Specified by:

getName in class GenericRepositoryObjectWrapper<PlateData>

Returns:

See above.

setName

public void setName(String name)

Sets the name of the plate.

Parameters:

name - The name of the plate. Mustn't be null.

Throws:

IllegalArgumentException - If the name is null.

asPlateData

@Deprecated
public PlateData asPlateData()

Deprecated.

Returns the PlateData contained. Use GenericObjectWrapper.asDataObject() instead.

Returns:

See above.

getDescription

public String getDescription()

Gets the plate description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<PlateData>

Returns:

See above.

setDescription

public void setDescription(String description)

Sets the description of the plate.

Parameters:

description - The description of the plate.

getScreens

public List<ScreenWrapper> getScreens(Client client)
                               throws OMEROServerError,
                                      ServiceException,
                                      AccessException,
                                      ExecutionException

Retrieves the screens containing this plate.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getPlateAcquisitions

public List<PlateAcquisitionWrapper> getPlateAcquisitions()

Returns the plate acquisitions related to this plate.

Returns:

See above.

getWells

public List<WellWrapper> getWells(Client client)
                           throws ServiceException,
                                  AccessException,
                                  ExecutionException

Gets all wells in the plate available from OMERO.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImages

public List<ImageWrapper> getImages(Client client)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Returns the images contained in the wells of this plate.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getColumnSequenceIndex

public int getColumnSequenceIndex()

Returns the index indicating how to label a column.

Returns:

See above.

getRowSequenceIndex

public int getRowSequenceIndex()

Returns the index indicating how to label a row.

Returns:

See above.

getDefaultSample

public int getDefaultSample()

Returns the currently selected field or 0.

Returns:

See above.

setDefaultSample

public void setDefaultSample(int value)

Sets the default sample.

Parameters:

value - The value to set.

getStatus

public String getStatus()

Returns the status of the plate.

Returns:

See above.

setStatus

public void setStatus(String value)

Sets the status.

Parameters:

value - The value to set.

getExternalIdentifier

public String getExternalIdentifier()

Returns the external identifier of the plate.

Returns:

See above.

setExternalIdentifier

public void setExternalIdentifier(String value)

Sets the external identifier.

Parameters:

value - The value to set.

getPlateType

public String getPlateType()

Returns the type of plate e.g. A 384-Well Plate, 96-Well Plate.

Returns:

See above.

getWellOriginX

public Length getWellOriginX(omero.model.enums.UnitsLength unit)
                      throws BigResult

Returns the x-coordinate in 2D-space of the well.

Parameters:

unit - The unit (can be null, in which case no conversion will be performed)

Returns:

See above

Throws:

BigResult - If an arithmetic under-/overflow occurred

getWellOriginY

public Length getWellOriginY(omero.model.enums.UnitsLength unit)
                      throws BigResult

Returns the y-coordinate in 2D-space of the well.

Parameters:

unit - The unit (can be null, in which case no conversion will be performed)

Returns:

See above

Throws:

BigResult - If an arithmetic under-/overflow occurred

refresh

public void refresh(Client client)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Reloads the plate from OMERO.

Parameters:

client - The client handling the connection.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.