net.sf.basedb.core
Class BioPlateType

java.lang.Object
  net.sf.basedb.core.BasicItem<BioPlateTypeData>
      net.sf.basedb.core.BioPlateType

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Removable

public class BioPlateType
extends BasicItem<BioPlateTypeData>
implements Nameable, Removable

This class represents the type of a bio-plate. This information can be used together with event definitions to create a work path in the lab. Eg. start with a plate of some type T1, then apply event E1 to it to get a new plate with type T2, repeat with event E2 to get a plate with type T3, and so on until the biomaterial has been hybridized.

Since:

2.16

Author:

Nicklas

Last modified

$Date: 2011-08-26 13:26:09 +0200 (Fri, 26 Aug 2011) $

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioPlateType(BioPlateTypeData data)

Method Summary

Item	getBioMaterialType() Get the biomaterial type that can be stored on plates of this type.
ItemQuery<BioPlate>	getBioPlates() Creates a query that returns all bioplates that are using this type.
static BioPlateType	getById(DbControl dc, int id) Gets a BioPlate type when knowing the item's id
String	getDescription() Get the description for the item.
ItemSubtype	getItemSubtype() Get the subtype that biomaterial items should have when placed on a plate with this bioplate type.
BioWell.LockMode	getLockMode() Get the lock mode for wells located on plates of this plate type.
String	getName() Get the name of the item.
static BioPlateType	getNew(DbControl dc) Creates a new bioplate type.
static ItemQuery<BioPlateType>	getQuery() Gets query that selects all available bioplates
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Gets all BioPlates and BioPlateEventDefinitions using this type
boolean	isRemoved() Check if the removed flag is set for this item.
boolean	isUsed() Check if there are any BioPlates or BioPlateEventDefinitions using this type.
void	setBioMaterialType(Item type) Set the type of biomaterial that can be stored on plates with this type.
void	setDescription(String description) Set the description for the item.
void	setItemSubtype(ItemSubtype subtype) Set the subtype that biomaterial items should have when placed on a plate with the bioplate type.
void	setLockMode(BioWell.LockMode lockMode) Set the lock mode for wells on plates of this plate type.
void	setName(String name) Set the name of the item.
void	setRemoved(boolean removed) Set the removed flag for this item.

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, initPermissions, 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

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

getId, getVersion

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

checkPermission, getPermissions, hasPermission

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOPLATETYPE, getType()

Constructor Detail

BioPlateType

BioPlateType(BioPlateTypeData data)

Method Detail

getNew

public static BioPlateType getNew(DbControl dc)
                           throws BaseException,
                                  InvalidDataException

Creates a new bioplate type.

Parameters:

dc - DbControl used for database access

Returns:

A new BioPlate object

Throws:

BaseException - If anything goes wrong when creating

InvalidDataException

getById

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

Gets a BioPlate type when knowing the item's id

Parameters:

dc - DbControl used for database access

id - The item's id.

Returns:

BioPlateType object

Throws:

ItemNotFoundException - If no item with the given id was found

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

BaseException - If there is another error.

getQuery

public static ItemQuery<BioPlateType> getQuery()

Gets query that selects all available bioplates

Returns:

ItemQuery object

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

getName

public String getName()

Description copied from interface: Nameable

Get the name of the item.

Specified by:

getName in interface Nameable

Returns:

A String with the name of the item

setName

public void setName(String name)
             throws PermissionDeniedException,
                    InvalidDataException

Description copied from interface: Nameable

Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the Nameable.MAX_NAME_LENGTH constant.

Specified by:

setName in interface Nameable

Parameters:

name - The new name for the item

Throws:

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

InvalidDataException - If the name is null or longer than specified by the Nameable.MAX_NAME_LENGTH constant

getDescription

public String getDescription()

Description copied from interface: Nameable

Get the description for the item.

Specified by:

getDescription in interface Nameable

Returns:

A String with a description of the item

setDescription

public void setDescription(String description)
                    throws PermissionDeniedException,
                           InvalidDataException

Description copied from interface: Nameable

Set the description for the item. The description can be null but mustn't be longer than the value specified by the Nameable.MAX_DESCRIPTION_LENGTH constant.

Specified by:

setDescription in interface Nameable

Parameters:

description - The new description for the item

Throws:

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

InvalidDataException - If the description longer than specified by the Nameable.MAX_DESCRIPTION_LENGTH constant

isRemoved

public boolean isRemoved()

Description copied from interface: Removable

Check if the removed flag is set for this item.

Specified by:

isRemoved in interface Removable

Returns:

TRUE if the item is flagged as removed, FALSE otherwise

setRemoved

public void setRemoved(boolean removed)
                throws PermissionDeniedException

Description copied from interface: Removable

Set the removed flag for this item.

Specified by:

setRemoved in interface Removable

Parameters:

removed - TRUE if the item should be flagged as removed, FALSE otherwise

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.DELETE permission for setting the flag to TRUE or Permission.WRITE permission for setting the flag to FALSE

isUsed

public boolean isUsed()

Check if there are any BioPlates or BioPlateEventDefinitions using this type.

Overrides:

isUsed in class BasicItem<BioPlateTypeData>

Returns:

TRUE if this item is used, FALSE otherwise

See Also:

BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Gets all BioPlates and BioPlateEventDefinitions using this type

Overrides:

getUsingItems in class BasicItem<BioPlateTypeData>

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)

getBioMaterialType

public Item getBioMaterialType()

Get the biomaterial type that can be stored on plates of this type.

Returns:

One of Item.SAMPLE, Item.EXTRACT or null if the plate can store mixed types

setBioMaterialType

public void setBioMaterialType(Item type)

Set the type of biomaterial that can be stored on plates with this type. Valid values are Item.SAMPLE, Item.EXTRACT, and null. The value can't be changed after the plate type has been saved to the database.

Parameters:

type - A biomaterial item type or null

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or if the plate type has already been saved to the database

InvalidDataException - If the type is not a biomaterial type

getItemSubtype

public ItemSubtype getItemSubtype()

Get the subtype that biomaterial items should have when placed on a plate with this bioplate type.

Returns:

A subtype or null if not important

Since:

3.0

setItemSubtype

public void setItemSubtype(ItemSubtype subtype)

Set the subtype that biomaterial items should have when placed on a plate with the bioplate type. A subtype can only be specified if a biomaterial type has been set and the given subtype must be compatible with the biomaterial type.

Parameters:

subtype - A subtype or null if the subtype is not important

Since:

3.0

getLockMode

public BioWell.LockMode getLockMode()

Get the lock mode for wells located on plates of this plate type. The lock mode determines if biomaterial may be changed in the well.

Returns:

A lock mode

setLockMode

public void setLockMode(BioWell.LockMode lockMode)

Set the lock mode for wells on plates of this plate type.

Parameters:

lockMode - A lock mode, null is not allowed

getBioPlates

public ItemQuery<BioPlate> getBioPlates()

Creates a query that returns all bioplates that are using this type.

Returns:

An ItemQuery object