net.sf.basedb.core
Class BioWell

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.ChildItem<BioWellData>
          net.sf.basedb.core.BioWell

All Implemented Interfaces:

AccessControlled, Identifiable

public class BioWell
extends ChildItem<BioWellData>

A biowell is located on a BioPlate and contains a MeasuredBioMaterial. The item holds information about witch row and column it is located on the bio plate.

Version:

2.10

Author:

Martin

See Also:

BioPlate

Last modified

$Date: 2008-11-27 16:33:55 +0100 (Thu, 27 Nov 2008) $

Nested Class Summary

static class

BioWell.LockMode The lock mode for a well is determined by the plate's bio plate type.

Field Summary

static Item

TYPE The type of item represented by this class.

Constructor Summary

BioWell(BioWellData data)

Method Summary

boolean	canAddBioMaterial() Check if it is possible to add/change biomaterial in this well.
boolean	canClearBioMaterial() Check if it is possible to clear the current biomaterial in this well.
MeasuredBioMaterial	getBioMaterial() Gets the MeasuredBioMaterial connected to this biowell.
static BioWell	getById(DbControl dc, int id) Get a BioWell item when you know the id.
int	getColumn() Gets the column index where this well is located.
String	getCoordinate() Get a string representation of the coordinate for this well.
BioWell.LockMode	getLockMode() Get the lock mode of this well.
MeasuredBioMaterial	getOriginalBioMaterial() Get the original biomaterial that was placed in this biowell.
BioPlate	getPlate() Get the BioPlate this biowell belongs to.
PlateCoordinate	getPlateCoordinate() Get the plate coordinate representation of the coordinate for this well.
static ItemQuery<BioWell>	getQuery(BioPlate bioPlate) Get a query configured to retrieve wells for a plate.
int	getRow() Gets the row index where this well is located.
(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() Adds the MeasuredBioMaterial,used in this well, to the Set.
boolean	hasBeenUsed() If the original biomaterial in this well has been moved to another plate (eg. for final storage in a freezer).
boolean	isEmpty() Is this well empty?
boolean	isUsed() Check if a MeasuredBioMaterial is linked to this bio-well

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

getPermissionForWriteDeleteAndCreate, getPluginPermissions, initPermissions

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate

Methods inherited from class java.lang.Object

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

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOWELL, getType()

Constructor Detail

BioWell

BioWell(BioWellData data)

Method Detail

getById

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

Get a BioWell 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 BioWell 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<BioWell> getQuery(BioPlate bioPlate)
                                   throws InvalidDataException

Get a query configured to retrieve wells for a plate. A plate is always required, but if a null bioplate parameter is used the query will include a parameter "bioPlate" that must be set before the query is actuall executed. The gain is that the same query can be re-used with multiple plates.

Parameters:

bioPlate - The plate to retreive wells for, null is allowed but a bioplate must be set for the "bioPlate" query parameter before the query is executed

Returns:

An ItemQuery object

Throws:

InvalidDataException

See Also:

Plate.getEvents()

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.

Returns:

A value indicating the type of item

getUsingItems

public Set<ItemProxy> getUsingItems()

Adds the MeasuredBioMaterial,used in this well, to the Set.

Overrides:

getUsingItems in class BasicItem<BioWellData>

Returns:

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

See Also:

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

isUsed

public boolean isUsed()
               throws BaseException

Check if a MeasuredBioMaterial is linked to this bio-well

Overrides:

isUsed in class BasicItem<BioWellData>

Returns:

TRUE if this biowell has a biomaterial connected., FALSE otherwise.

Throws:

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

See Also:

BasicItem.getUsingItems()

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<BioWellData>

Returns:

The parent item

getPlate

public BioPlate getPlate()
                  throws PermissionDeniedException,
                         BaseException

Get the BioPlate this biowell belongs to.

Returns:

The BioPlate item

Throws:

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

BaseException - If there is another error

getBioMaterial

public MeasuredBioMaterial getBioMaterial()
                                   throws PermissionDeniedException,
                                          BaseException

Gets the MeasuredBioMaterial connected to this biowell.

Returns:

a MeasuredBioMaterial item or null.

Throws:

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

BaseException - If there is another error

getRow

public int getRow()

Gets the row index where this well is located.

Returns:

Row number as an int

getColumn

public int getColumn()

Gets the column index where this well is located.

Returns:

Column number as an int

getPlateCoordinate

public PlateCoordinate getPlateCoordinate()

Get the plate coordinate representation of the coordinate for this well.

Returns:

A PlateCoordinate object

Since:

2.17

getCoordinate

public String getCoordinate()

Get a string representation of the coordinate for this well. Rows are mapped to letters (0-A, 1-B, etc.). Columns are mapped to 1-based numbers (0-1, 1-2, etc.)

Since:

2.16

isEmpty

public boolean isEmpty()

Is this well empty?

Since:

2.16

getLockMode

public BioWell.LockMode getLockMode()

Get the lock mode of this well. The lock mode determines if it is possible to add biomaterial to an empty well or remove biomaterial from the well.

Returns:

The lock mode as determined by the plate's plate type

Since:

2.16

canAddBioMaterial

public boolean canAddBioMaterial()

Check if it is possible to add/change biomaterial in this well.

Returns:

TRUE if it is possible to add biomaterial to the well, FALSE otherwise

Since:

2.16

See Also:

BioWell.LockMode.canAdd(BioWell)

canClearBioMaterial

public boolean canClearBioMaterial()

Check if it is possible to clear the current biomaterial in this well.

Returns:

TRUE if it is possible to clear the well

Since:

2.16

See Also:

BioWell.LockMode.canClear(BioWell)

hasBeenUsed

public boolean hasBeenUsed()

If the original biomaterial in this well has been moved to another plate (eg. for final storage in a freezer). This property is only defined for well with lock mode=BioWell.LockMode.LOCKED_AFTER_MOVE.

Returns:

TRUE if the original biomaterial has been moved

Since:

2.16

getOriginalBioMaterial

public MeasuredBioMaterial getOriginalBioMaterial()

Get the original biomaterial that was placed in this biowell. This property is only defined for well with lock mode=BioWell.LockMode.LOCKED_AFTER_MOVE after the biomaterial has been moved.

Returns:

The original biomaterial

Since:

2.16