Package net.sf.basedb.core

Class PlateGeometry

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.PlateGeometry

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Registered, Removable

public class PlateGeometry
extends BasicItem
implements Nameable, Removable, Registered

This class defines a plate geometry, which is the number of rows and columns of wells on a Plate. The number of rows and columns must be specified when the item is created, and the values can't be changed after that.

A PlateMapping is a way to specify how one geometry can be transformed to another. It holds information for how to map all source wells to destination wells. For example it can map four 96-well plates to one 384-well plate.

Version:

2.0

Author:

Nicklas

See Also:

• Plate
• PlateMapping

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.

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Constructors

Constructor	Description
PlateGeometry(PlateGeometryData plateGeometryData)

Method Summary

Modifier and Type	Method	Description
static PlateGeometry	getById(DbControl dc, int id)	Get a PlateGeometry item when you know the id.
int	getColumns()	Get the number of columns in this geometry.
(package private) PlateGeometryData	getData()	Get the BasicData object that holds all data for this item.
String	getDescription()	Get the description for the item.
Date	getEntryDate()	Get the date that the item was registered in the database.
String	getName()	Get the name of the item.
static PlateGeometry	getNew(DbControl dc, int rows, int columns)	Create a new PlateGeometry item.
ItemQuery<PlateType>	getPlateTypes()	Get a query returning all plate types using this geometry.
static ItemQuery<PlateGeometry>	getQuery()	Get a query configured to retrieve plate geometries.
User	getRemovedBy()	Get the user that flagged this item for removal.
int	getRows()	Get the number of rows in this geometry.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: PlateType:s of this geometry PlateMapping:s using this geometry BioPlate:s using this geometry
boolean	isRemoved()	Check if the removed flag is set for this item.
boolean	isUsed()	Check if: A PlateType with this geometry exists A PlateMapping to/from this geometry exists A BioPlate that uses this geometry exists
PlateType	newPlateType()	Create a new PlateType of this geometry.
private void	setColumns(int columns)	The number of columns cannot be changed, used at object creation only.
void	setDescription(String description)	Set the description for the item.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setName(String name)	Set the name of the item.
void	setRemoved(boolean removed)	Set the removed flag for this item.
private void	setRows(int rows)	The number of rows cannot be changed, used at object creation only.

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, initPermissions, 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.PLATEGEOMETRY
• getType()

Constructor Details

PlateGeometry

PlateGeometry(PlateGeometryData plateGeometryData)

Method Details

getNew

public static PlateGeometry getNew(DbControl dc,
 int rows,
 int columns)
                            throws InvalidDataException,
BaseException

Create a new PlateGeometry item.

Parameters:

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

rows - The number of rows

columns - The number of columns

Returns:

The new PlateGeometry item

Throws:

InvalidDataException - If the number of rows or columns is less than or equal to zero

BaseException - If there is an error

getById

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

Get a PlateGeometry 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 PlateGeometry 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<PlateGeometry> getQuery()

Get a query configured to retrieve plate geometries.

Returns:

An ItemQuery object

getData

PlateGeometryData 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

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

getRemovedBy

public User getRemovedBy()
                  throws PermissionDeniedException,
ItemNotFoundException

Description copied from interface: Removable

Get the user that flagged this item for removal.

Specified by:

getRemovedBy in interface Removable

Returns:

A User object, or null if this item has not been flagged

Throws:

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

ItemNotFoundException - If the user that removed this item can't be found

getEntryDate

public Date getEntryDate()

Description copied from interface: Registered

Get the date that the item was registered in the database.

Specified by:

getEntryDate in interface Registered

Returns:

A date or null if this is not known

setEntryDate

public void setEntryDate(Date entryDate)

Description copied from interface: Registered

Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.

Specified by:

setEntryDate in interface Registered

Parameters:

entryDate - A date or null to use today's date

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• A PlateType with this geometry exists
• A PlateMapping to/from this geometry exists
• A BioPlate that uses this geometry exists

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:

• PlateType:s of this geometry
• PlateMapping:s using this geometry
• BioPlate:s using this geometry

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)

getRows

public int getRows()

Get the number of rows in this geometry.

Returns:

The number of rows

setRows

private void setRows(int rows)
              throws InvalidDataException

The number of rows cannot be changed, used at object creation only.

Throws:

InvalidDataException - If the row count is less than 1

getColumns

public int getColumns()

Get the number of columns in this geometry.

Returns:

The number of columns

setColumns

private void setColumns(int columns)
                 throws InvalidDataException

The number of columns cannot be changed, used at object creation only.

Throws:

InvalidDataException - If the column count is less than 1

newPlateType

public PlateType newPlateType()
                       throws PermissionDeniedException,
BaseException

Create a new PlateType of this geometry.

Returns:

The new plate type

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this plate geometry

BaseException - If there is another error

getPlateTypes

public ItemQuery<PlateType> getPlateTypes()

Get a query returning all plate types using this geometry.

Returns:

An ItemQuery