Package fr.igred.omero.screen

Class PlateWrapper

java.lang.Object

fr.igred.omero.ObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

fr.igred.omero.RepositoryObjectWrapper<PlateData>

fr.igred.omero.screen.PlateWrapper

All Implemented Interfaces:

Annotatable, HCSLinked, ImageLinked, RemoteObject, RepositoryObject, Plate

public class PlateWrapper
extends RepositoryObjectWrapper<PlateData>
implements Plate

Class containing a PlateData object.

Wraps function calls to the PlateData contained.

Field Summary

Fields

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

Fields inherited from class fr.igred.omero.ObjectWrapper

data

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected java.lang.String	annotationLinkType()	Returns the type of annotation link for this object.
int	getColumnSequenceIndex()	Returns the index indicating how to label a column.
int	getDefaultSample()	Returns the currently selected field or 0.
java.lang.String	getDescription()	Gets the plate description
java.lang.String	getExternalIdentifier()	Returns the external identifier of the plate.
java.lang.String	getName()	Gets the plate name.
java.util.List<PlateAcquisition>	getPlateAcquisitions()	Returns the plate acquisitions related to this plate.
java.lang.String	getPlateType()	Returns the type of plate e.g.
int	getRowSequenceIndex()	Returns the index indicating how to label a row.
java.lang.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.
java.util.List<Well>	getWells(Browser browser)	Gets all wells in the plate available from OMERO.
void	reload(Browser browser)	Reloads the plate from OMERO.
void	setDefaultSample(int value)	Sets the default sample.
void	setDescription(java.lang.String description)	Sets the description of the plate.
void	setExternalIdentifier(java.lang.String value)	Sets the external identifier.
void	setName(java.lang.String name)	Sets the name of the plate.
void	setStatus(java.lang.String value)	Sets the status.

Methods inherited from class fr.igred.omero.RepositoryObjectWrapper

importImage, importImages

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceTable, addKeyValuePair, addTag, addTag, getAnnotations, getFileAnnotations, getMapAnnotations, getMyRating, getTable, getTags, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.ObjectWrapper

asDataObject, canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, 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

Methods inherited from interface fr.igred.omero.Annotatable

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addKeyValuePair, addTable, addTag, addTag, addTags, copyAnnotationLinks, getAnnotationData, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getTable, getTables, getTags, getValues, isLinked, link, link, linkIfNotLinked, rate, unlink

Methods inherited from interface fr.igred.omero.screen.Plate

asDataObject, getImages, getPlateAcquisitions, getPlates, getScreens

Methods inherited from interface fr.igred.omero.RemoteObject

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, getCreated, getGroupId, getId, getOwner, saveAndUpdate

Field Detail

ANNOTATION_LINK

public static final java.lang.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 java.lang.String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<PlateData>

Returns:

See above.

getName

public java.lang.String getName()

Gets the plate name.

Specified by:

getName in interface RepositoryObject

Returns:

See above.

setName

public void setName(java.lang.String name)

Sets the name of the plate.

Specified by:

setName in interface Plate

Parameters:

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

Throws:

java.lang.IllegalArgumentException - If the name is null.

getDescription

public java.lang.String getDescription()

Gets the plate description

Specified by:

getDescription in interface RepositoryObject

Returns:

See above.

setDescription

public void setDescription(java.lang.String description)

Sets the description of the plate.

Specified by:

setDescription in interface Plate

Parameters:

description - The description of the plate.

getPlateAcquisitions

public java.util.List<PlateAcquisition> getPlateAcquisitions()

Returns the plate acquisitions related to this plate.

Specified by:

getPlateAcquisitions in interface Plate

Returns:

See above.

getWells

public java.util.List<Well> getWells(Browser browser)
                              throws ServiceException,
                                     AccessException,
                                     java.util.concurrent.ExecutionException

Gets all wells in the plate available from OMERO.

Specified by:

getWells in interface HCSLinked

Specified by:

getWells in interface Plate

Parameters:

browser - The data browser.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getColumnSequenceIndex

public int getColumnSequenceIndex()

Returns the index indicating how to label a column.

Specified by:

getColumnSequenceIndex in interface Plate

Returns:

See above.

getRowSequenceIndex

public int getRowSequenceIndex()

Returns the index indicating how to label a row.

Specified by:

getRowSequenceIndex in interface Plate

Returns:

See above.

getDefaultSample

public int getDefaultSample()

Returns the currently selected field or 0.

Specified by:

getDefaultSample in interface Plate

Returns:

See above.

setDefaultSample

public void setDefaultSample(int value)

Sets the default sample.

Specified by:

setDefaultSample in interface Plate

Parameters:

value - The value to set.

getStatus

public java.lang.String getStatus()

Returns the status of the plate.

Specified by:

getStatus in interface Plate

Returns:

See above.

setStatus

public void setStatus(java.lang.String value)

Sets the status.

Specified by:

setStatus in interface Plate

Parameters:

value - The value to set.

getExternalIdentifier

public java.lang.String getExternalIdentifier()

Returns the external identifier of the plate.

Specified by:

getExternalIdentifier in interface Plate

Returns:

See above.

setExternalIdentifier

public void setExternalIdentifier(java.lang.String value)

Sets the external identifier.

Specified by:

setExternalIdentifier in interface Plate

Parameters:

value - The value to set.

getPlateType

public java.lang.String getPlateType()

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

Specified by:

getPlateType in interface 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.

Specified by:

getWellOriginX in interface Plate

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.

Specified by:

getWellOriginY in interface Plate

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

reload

public void reload(Browser browser)
            throws ServiceException,
                   AccessException,
                   java.util.concurrent.ExecutionException

Reloads the plate from OMERO.

Specified by:

reload in interface Plate

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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