Package net.sf.basedb.core

Class Well

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.Well

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable

public class Well
extends ChildItem
implements Annotatable

A well is located on a Plate and contains a ReporterData. If the plate the well is located on was created from some other plates via a PlateMapping the well also contains a reference back to the parent well on one of the source plates.

Once the well has been saved to the database it cannot be modified, except for annotations.

Version:

2.0

Author:

Nicklas

See Also:

• Plate

Last modified

$Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $

Field Summary

Fields

Modifier and Type	Field	Description
static final Item	TYPE	The type of item represented by this class.

Constructor Summary

Constructors

Constructor	Description
Well(WellData wellData)

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get the parent well, if any.
AnnotationSet	getAnnotationSet()	Get the annotation set containing the annotations for this item.
static Well	getById(DbControl dc, int id)	Get a Well item when you know the id.
int	getColumn()	Get the column coordinate of this well on the plate.
(package private) WellData	getData()	Get the BasicData object that holds all data for this item.
Well	getParent()	Get the parent well.
Plate	getPlate()	Get the Plate this event belongs to.
Protocol	getProtocol()	A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.
static ItemQuery<Well>	getQuery(Plate plate)	Get a query configured to retrieve wells for a plate.
ReporterData	getReporter()	Get the reporter in this well.
ReporterData	getReporter(boolean forceInitialization)	Get the reporter in this well.
int	getRow()	Get the row coordinate of this well on the plate.
(package private) SharedData	getSharedParent()	Get the shareable parent item of this child item.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: Child wells Features derived from this well
boolean	isAnnotated()	Check if this item has an annotation set.
boolean	isUsed()	Check if: a Feature is linked to this well another Well has this well as it's parent well
void	removeAnnotations()	Remove all annotations from this item, by deleting the annotation set.
(package private) void	setParent(Well parent)	Set the parent well.
void	setReporter(ReporterData reporter)	Set the reporter of this well.

Methods inherited from class net.sf.basedb.core.ChildItem

getPermissionForUse, getPermissionForWriteDeleteAndCreate, getPluginPermissions, initPermissions

Methods inherited from class net.sf.basedb.core.BasicItem

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.WELL
• getType()

Constructor Details

Well

Well(WellData wellData)

Method Details

getById

public static Well getById(DbControl dc,
 int id)
                    throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a Well item when you know the id.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The id of the item to load

Returns:

The Well item

Throws:

ItemNotFoundException - If an item with the specified id is not found

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<Well> getQuery(Plate plate)
                                throws InvalidDataException

Get a query configured to retrieve wells for a plate.

Parameters:

plate - The plate to retreive wells for, null is not allowed

Returns:

An ItemQuery object

Throws:

InvalidDataException - If required parameter is null.

See Also:

• Plate.getEvents()

getData

WellData getData()

Description copied from class: BasicItem

Get the BasicData object that holds all data for this item.

Specified by:

getData in class BasicItem

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

getAnnotationSet

public AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Get the annotation set containing the annotations for this item. If the item doesn't have any annotations a new annotation set is created and automatically saved to the database when DbControl.commit() is called. To check if an item has annotations without creating a new annotation set use the Annotatable.isAnnotated() method.

Specified by:

getAnnotationSet in interface Annotatable

Returns:

An AnnotationSet

Throws:

PermissionDeniedException - If the logged in user doesn't have enough permissions

BaseException - If there is another error

isAnnotated

public boolean isAnnotated()

Description copied from interface: Annotatable

Check if this item has an annotation set. The annotation set may be empty.

Specified by:

isAnnotated in interface Annotatable

Returns:

TRUE if an annotation set exists, FALSE otherwise

removeAnnotations

public void removeAnnotations()
                       throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Remove all annotations from this item, by deleting the annotation set.

Specified by:

removeAnnotations in interface Annotatable

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is another error

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the parent well, if any.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getProtocol

public Protocol getProtocol()

Description copied from interface: Annotatable

A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.

Specified by:

getProtocol in interface Annotatable

Returns:

Always null

Since:

2.2

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• a Feature is linked to this well
• another Well has this well as it's parent well

Overrides:

isUsed in class BasicItem

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException - If not able to tell if item is used or not.

See Also:

• BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• Child wells
• Features derived from this well

Overrides:

getUsingItems in class BasicItem

Returns:

A set containing proxies for the items, or an empty set if no items are using this item

Since:

2.2

See Also:

• BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)

getSharedParent

SharedData getSharedParent()

Description copied from class: ChildItem

Get the shareable parent item of this child item. This is used by the ChildItem.initPermissions(int, int) method to calculate the logged in user's permissions for the child item.

Specified by:

getSharedParent in class ChildItem

Returns:

The parent item

getPlate

public Plate getPlate()
               throws PermissionDeniedException,
BaseException

Get the Plate this event belongs to.

Returns:

The Plate item

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission for the plate

BaseException - If there is another error

getRow

public int getRow()

Get the row coordinate of this well on the plate.

getColumn

public int getColumn()

Get the column coordinate of this well on the plate.

getParent

public Well getParent()
               throws PermissionDeniedException,
BaseException

Get the parent well. The parent well is one of the wells on one of the parent plates if the plate this well is on was created by a PlateMapping.

Returns:

A Well item or null if this plate has no parents

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the parent well

BaseException - If there is another error

setParent

void setParent(Well parent)

Set the parent well. Used by PlateMapping when creating new plates from a mapping. This method also sets the reporter to the same reporter as the parent well.

getReporter

public ReporterData getReporter()
                         throws PermissionDeniedException,
BaseException

Get the reporter in this well.

Returns:

A ReporterData object or null if no reporter has been specified

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to reporters

BaseException - If there is another error

getReporter

public ReporterData getReporter(boolean forceInitialization)

Get the reporter in this well. The initialization of the reporter can be forced.

Parameters:

forceInitialization - TRUE if the initialization of the reporter should be forced, FALSE otherwise.

Returns:

A ReporterData object or null if no reporter has been specified.

Since:

2.13

setReporter

public void setReporter(ReporterData reporter)
                 throws PermissionDeniedException

Set the reporter of this well.

Parameters:

reporter - The new reporter or null if the reporter is unknown

Throws:

PermissionDeniedException - If this well has been saved to the database or a parent well has been set (in which case the reporter must always be the same as for the parent) or the logged in user doesn't have write permission for the well or use permission for reporters