Package fr.igred.omero.repository

Class FolderWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

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

fr.igred.omero.repository.FolderWrapper

public class FolderWrapper
extends GenericRepositoryObjectWrapper<FolderData>

Class containing a FolderData object.

Wraps function calls to the FolderData 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
FolderWrapper(Client client, String name)	Constructor of the FolderWrapper class.
FolderWrapper(FolderData folder)	Constructor of the FolderWrapper class.
FolderWrapper(Folder folder)	Constructor of the FolderWrapper class.

Method Summary

Modifier and Type	Method	Description
void	addChild(FolderWrapper folder)	Adds a child folder to this folder.
void	addChildren(Collection<? extends FolderWrapper> folders)	Adds children folders to this folder.
void	addImages(Client client, ImageWrapper... images)	Links images to the folder in OMERO.
void	addROI(Client client, ROIWrapper roi)	Deprecated. Adds an ROI to the folder and associate it to the image id set(an image need to be associated)
void	addROIs(Client client, long imageId, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image ID.
void	addROIs(Client client, ImageWrapper image, ROIWrapper... rois)	Adds ROIs to the folder and associate them to the provided image.
protected String	annotationLinkType()	Returns the type of annotation link for this object.
FolderData	asFolderData()	Deprecated. Gets the folder contained in the FolderWrapper.
List<FolderWrapper>	getChildren()	Retrieves the children folders for this folder.
String	getDescription()	Gets the folder description
List<ImageWrapper>	getImages()	Retrieves the images contained in this folder.
List<ImageWrapper>	getImages(Client client)	Retrieves the images contained in this folder.
String	getName()	Gets the name of the folder
FolderWrapper	getParent()	Retrieves the parent folders for this folder.
List<ROIWrapper>	getROIs(Client client)	Deprecated. Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
List<ROIWrapper>	getROIs(Client client, long imageId)	Gets the ROIs contained in the folder associated with the provided image ID.
List<ROIWrapper>	getROIs(Client client, ImageWrapper image)	Gets the ROIs contained in the folder associated with the provided image.
protected <A extends AnnotationData> void	link(Client client, A annotation)	Adds an annotation to the object in OMERO, if possible.
void	reload(Browser browser)	Reloads the folder from OMERO, to update all links.
void	reload(Client client)	Deprecated. Reloads the folder from OMERO, to update all links.
void	setDescription(String description)	Sets the description of the folder.
void	setImage(long id)	Deprecated. Sets the image associated to the folder
void	setImage(ImageWrapper image)	Deprecated. Sets the image associated to the folder
void	setName(String name)	Sets the name of the folder.
void	setParent(FolderWrapper folder)	Sets the parent folder for this folder.
void	unlinkAllROI(Client client)	Deprecated. Unlink all ROI, associated to the image set, in the folder.
void	unlinkAllROIs(Client client)	Unlink all ROIs associated to this folder.
void	unlinkAllROIs(Client client, long imageId)	Unlink all ROIs associated to the provided image ID from the folder.
void	unlinkAllROIs(Client client, ImageWrapper image)	Unlink all ROIs associated to the provided image from the folder.
void	unlinkROI(Client client, ROIWrapper roi)	Deprecated. Unlink an ROI, associated to the image set, in the folder.
void	unlinkROIs(Client client, ROIWrapper... rois)	Unlink ROIs from the folder.
void	unlinkROIs(Client client, Collection<? extends ROIWrapper> rois)	Unlink ROIs from the folder.

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

FolderWrapper

public FolderWrapper(FolderData folder)

Constructor of the FolderWrapper class.

Parameters:

folder - The FolderData to wrap.

FolderWrapper

public FolderWrapper(Folder folder)

Constructor of the FolderWrapper class.

Parameters:

folder - Folder to contain.

FolderWrapper

public FolderWrapper(Client client,
 String name)
              throws ServiceException,
OMEROServerError

Constructor of the FolderWrapper class. Save the folder in OMERO

Parameters:

client - The client handling the connection.

name - Name of the folder.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

Method Details

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<FolderData>

Returns:

See above.

link

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

Adds an annotation to the object in OMERO, if possible.

Overrides:

link in class AnnotatableWrapper<FolderData>

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - Annotation to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getName

public String getName()

Gets the name of the folder

Specified by:

getName in class GenericRepositoryObjectWrapper<FolderData>

Returns:

name.

setName

public void setName(String name)

Sets the name of the folder.

Parameters:

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

Throws:

IllegalArgumentException - If the name is null.

asFolderData

@Deprecated
public FolderData asFolderData()

Deprecated.

Gets the folder contained in the FolderWrapper. Use GenericObjectWrapper.asDataObject() instead.

Returns:

the FolderData.

getDescription

public String getDescription()

Gets the folder description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<FolderData>

Returns:

The folder description.

setDescription

public void setDescription(String description)

Sets the description of the folder.

Parameters:

description - The folder description.

reload

@Deprecated
public void reload(Client client)
            throws AccessException,
ServiceException,
ExecutionException

Deprecated.

Reloads the folder from OMERO, to update all links.

Parameters:

client - The client handling the connection.

Throws:

AccessException - Cannot access data.

ServiceException - Cannot connect to OMERO.

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

getParent

public FolderWrapper getParent()

Retrieves the parent folders for this folder.

Returns:

See above

setParent

public void setParent(FolderWrapper folder)

Sets the parent folder for this folder.

Parameters:

folder - The new parent folder.

addChild

public void addChild(FolderWrapper folder)

Adds a child folder to this folder.

Parameters:

folder - The new child folder.

addChildren

public void addChildren(Collection<? extends FolderWrapper> folders)

Adds children folders to this folder.

Parameters:

folders - The new children folders.

getChildren

public List<FolderWrapper> getChildren()

Retrieves the children folders for this folder.

Returns:

See above

addImages

public void addImages(Client client,
 ImageWrapper... images)
               throws ServiceException,
AccessException,
ExecutionException

Links images to the folder in OMERO.

Parameters:

client - The client handling the connection.

images - Images to add.

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 this folder.

Returns:

See above

getImages

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

Retrieves the images contained in this folder.

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.

setImage

@Deprecated
public void setImage(long id)

Deprecated.

Sets the image associated to the folder

Parameters:

id - ID of the image to associate.

setImage

@Deprecated
public void setImage(ImageWrapper image)

Deprecated.

Sets the image associated to the folder

Parameters:

image - Image to associate.

addROI

@Deprecated
public void addROI(Client client,
 ROIWrapper roi)
            throws ServiceException,
AccessException,
ExecutionException

Deprecated.

Adds an ROI to the folder and associate it to the image id set(an image need to be associated)

Parameters:

client - The client handling the connection.

roi - ROI to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - If the ROIFacility can't be retrieved or instantiated.

addROIs

public void addROIs(Client client,
 long imageId,
 ROIWrapper... rois)
             throws ServiceException,
AccessException,
ExecutionException

Adds ROIs to the folder and associate them to the provided image ID.

Parameters:

client - The client handling the connection.

imageId - The image ID.

rois - ROIs to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - If the ROIFacility can't be retrieved or instantiated.

addROIs

public void addROIs(Client client,
 ImageWrapper image,
 ROIWrapper... rois)
             throws ServiceException,
AccessException,
ExecutionException

Adds ROIs to the folder and associate them to the provided image.

Parameters:

client - The client handling the connection.

image - The image.

rois - ROIs to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - If the ROIFacility can't be retrieved or instantiated.

getROIs

@Deprecated
public List<ROIWrapper> getROIs(Client client)
                         throws ServiceException,
AccessException,
ExecutionException

Deprecated.

Gets the ROI contained in the folder associated with the image id set (an image need to be associated)

Parameters:

client - The client handling the connection.

Returns:

List of ROIWrapper containing the ROI.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getROIs

public List<ROIWrapper> getROIs(Client client,
 long imageId)
                         throws ServiceException,
AccessException,
ExecutionException

Gets the ROIs contained in the folder associated with the provided image ID.

Parameters:

client - The client handling the connection.

imageId - The image.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getROIs

public List<ROIWrapper> getROIs(Client client,
 ImageWrapper image)
                         throws ServiceException,
AccessException,
ExecutionException

Gets the ROIs contained in the folder associated with the provided image.

Parameters:

client - The client handling the connection.

image - The image.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

unlinkAllROI

@Deprecated
public void unlinkAllROI(Client client)
                  throws ServiceException,
AccessException,
ExecutionException

Deprecated.

Unlink all ROI, associated to the image set, in the folder. ROIs are now linked to the image directly

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.

unlinkAllROIs

public void unlinkAllROIs(Client client,
 long imageId)
                   throws ServiceException,
AccessException,
ExecutionException

Unlink all ROIs associated to the provided image ID from the folder.

ROIs are now linked to the image directly.

Parameters:

client - The client handling the connection.

imageId - The image ID.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

unlinkAllROIs

public void unlinkAllROIs(Client client,
 ImageWrapper image)
                   throws ServiceException,
AccessException,
ExecutionException

Unlink all ROIs associated to the provided image from the folder.

ROIs are now linked to the image directly.

Parameters:

client - The client handling the connection.

image - The image.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

unlinkAllROIs

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

Unlink all ROIs associated to this folder.

The folder must be loaded beforehand.

ROIs are now linked to their images directly.

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.

unlinkROI

@Deprecated
public void unlinkROI(Client client,
 ROIWrapper roi)
               throws ServiceException,
AccessException,
ExecutionException

Deprecated.

Unlink an ROI, associated to the image set, in the folder. The ROI is now linked to the image directly.

Parameters:

client - The client handling the connection.

roi - ROI to unlink.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

unlinkROIs

public void unlinkROIs(Client client,
 ROIWrapper... rois)
                throws ServiceException,
AccessException,
ExecutionException

Unlink ROIs from the folder.

The ROIs are now linked to the image directly.

Parameters:

client - The data manager.

rois - ROI to unlink.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

unlinkROIs

public void unlinkROIs(Client client,
 Collection<? extends ROIWrapper> rois)
                throws ServiceException,
AccessException,
ExecutionException

Unlink ROIs from the folder.

The ROIs are now linked to the image directly.

Parameters:

client - The data manager.

rois - ROI to unlink.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

reload

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

Reloads the folder from OMERO, to update all links.

Overrides:

reload in class GenericRepositoryObjectWrapper<FolderData>

Parameters:

browser - The data browser.

Throws:

AccessException - Cannot access data.

ServiceException - Cannot connect to OMERO.

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