Package fr.igred.omero.repository

Class PlateAcquisitionWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

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

fr.igred.omero.repository.PlateAcquisitionWrapper

public class PlateAcquisitionWrapper
extends GenericRepositoryObjectWrapper<PlateAcquisitionData>

Class containing a PlateAcquisitionData object.

Wraps function calls to the PlateAcquisitionData 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 final 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
PlateAcquisitionWrapper(PlateAcquisitionData plateAcquisition)	Constructor of the class PlateAcquisitionWrapper.

Method Summary

Modifier and Type	Method	Description
protected String	annotationLinkType()	Returns the type of annotation link for this object.
PlateAcquisitionData	asPlateAcquisitionData()	Deprecated. Returns the PlateAcquisitionData contained.
String	getDescription()	Gets the plate acquisition description
Timestamp	getEndTime()	Returns the time when the last image was collected.
List<ImageWrapper>	getImages()	Retrieves the images contained in the well samples.
List<ImageWrapper>	getImages(Client client)	Retrieves the images contained in the wells in the parent plate.
String	getLabel()	Returns the label associated to the plate acquisition.
int	getMaximumFieldCount()	Returns the maximum number of fields in any well.
String	getName()	Gets the plate acquisition name.
List<PlateWrapper>	getPlates(Client client)	Returns the (updated) parent plate as a singleton list.
long	getRefPlateId()	Returns the id of the plate of reference.
List<ScreenWrapper>	getScreens(Client client)	Retrieves the screens containing the parent plates.
Timestamp	getStartTime()	Returns the time when the first image was collected.
List<WellWrapper>	getWells(Client client)	Retrieves the wells contained in the parent plate.
List<WellSampleWrapper>	getWellSamples()	Retrieves the well samples for this plate acquisition.
List<WellSampleWrapper>	getWellSamples(Browser browser)	Retrieves the well samples for this plate acquisition from OMERO and updates the object.
protected <A extends AnnotationData> void	link(Client client, A annotation)	Adds a tag to the object in OMERO, if possible.
void	reload(Browser browser)	Reloads the plate acquisition from OMERO.
void	setDescription(String description)	Sets the description of the plate acquisition.
void	setName(String name)	Sets the name of the plate acquisition.
void	setRefPlateId(long refPlateId)	Sets the id of the plate this plate acquisition is for.

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

copyAnnotationLinks, importImage, importImages, refresh

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, getRatings, 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, getUpdated, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

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

Field Details

ANNOTATION_LINK

public static final String ANNOTATION_LINK

Annotation link name for this type of object

See Also:

• Constant Field Values

Constructor Details

PlateAcquisitionWrapper

public PlateAcquisitionWrapper(PlateAcquisitionData plateAcquisition)

Constructor of the class PlateAcquisitionWrapper.

Parameters:

plateAcquisition - The PlateAcquisitionData to wrap in the PlateAcquisitionWrapper.

Method Details

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<PlateAcquisitionData>

Returns:

See above.

getName

public String getName()

Gets the plate acquisition name.

Specified by:

getName in class GenericRepositoryObjectWrapper<PlateAcquisitionData>

Returns:

See above.

setName

public void setName(String name)

Sets the name of the plate acquisition.

Parameters:

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

Throws:

IllegalArgumentException - If the name is null.

asPlateAcquisitionData

@Deprecated
public PlateAcquisitionData asPlateAcquisitionData()

Deprecated.

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

Returns:

See above.

getDescription

public String getDescription()

Gets the plate acquisition description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<PlateAcquisitionData>

Returns:

See above.

setDescription

public void setDescription(String description)

Sets the description of the plate acquisition.

Parameters:

description - The description of the plate acquisition.

link

protected <A extends AnnotationData> void link(Client client,
 A annotation)
                                        throws ServiceException,
AccessException,
ExecutionException

Adds a tag to the object in OMERO, if possible.

Overrides:

link in class AnnotatableWrapper<PlateAcquisitionData>

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - Tag to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getScreens

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

Retrieves the screens containing the parent plates.

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.

OMEROServerError - Server error.

getPlates

public List<PlateWrapper> getPlates(Client client)
                             throws ServiceException,
AccessException,
ExecutionException

Returns the (updated) parent plate as a singleton list.

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.

getWells

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

Retrieves the wells contained in the parent 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.

getWellSamples

public List<WellSampleWrapper> getWellSamples()

Retrieves the well samples for this plate acquisition.

Returns:

See above.

getWellSamples

public List<WellSampleWrapper> getWellSamples(Browser browser)
                                       throws AccessException,
ServiceException,
ExecutionException

Retrieves the well samples for this plate acquisition from OMERO and updates the object.

Parameters:

browser - The data browser.

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()

Retrieves the images contained in the well samples.

Returns:

See above

getImages

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

Retrieves the images contained in the wells in the parent 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.

getLabel

public String getLabel()

Returns the label associated to the plate acquisition.

Returns:

See above.

getRefPlateId

public long getRefPlateId()

Returns the id of the plate of reference.

Returns:

See above.

setRefPlateId

public void setRefPlateId(long refPlateId)

Sets the id of the plate this plate acquisition is for.

Parameters:

refPlateId - The value to set.

getStartTime

public Timestamp getStartTime()

Returns the time when the first image was collected.

Returns:

See above.

getEndTime

public Timestamp getEndTime()

Returns the time when the last image was collected.

Returns:

See above.

getMaximumFieldCount

public int getMaximumFieldCount()

Returns the maximum number of fields in any well.

Returns:

See above.

reload

public void reload(Browser browser)
            throws ServiceException,
AccessException,
ExecutionException

Reloads the plate acquisition from OMERO.

Overrides:

reload in class GenericRepositoryObjectWrapper<PlateAcquisitionData>

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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