Package net.sf.basedb.core

Class PlateMapping

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.OwnedItem

net.sf.basedb.core.SharedItem

net.sf.basedb.core.CommonItem

net.sf.basedb.core.PlateMapping

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Registered, Removable, Shareable

public class PlateMapping
extends CommonItem
implements Registered

This class represents a mapping from one plate geometry to another. Given one or more plates of some specific geometry, a mapping creates one or more new plates of some other or the same geometry. The new plates and their wells will be linked to the plates and wells they were created from.

A mapping is specified by a set of source/destination coordinate pairs. A coordinate is specified by plate number, row and column. With this information it is possible to pick wells from the source plates and link them to wells on the destination plates.

It is not required that the mapping is complete, ie. contains a mapping for each destination coordinate. Such destination wells will be marked as empty. A destination coordinate may only be mapped to one source coordinate, but it is possible that one source coordinate is mapped to several destination coordinates.

Version:

2.0

Author:

Nicklas

See Also:

Plate, PlateGeometry

Last modified

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

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAX_IMAGE_LENGTH	The maximum length of the image name that can be stored in the database.
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

Constructors

Constructor	Description
PlateMapping(PlateMappingData plateMappingData)

Method Summary

Modifier and Type	Method	Description
List<Plate>	apply(List<Plate> sourcePlates, PlateType destinationPlateType)	Apply this mapping to the given list of source plates and generate new plates of the specified type.
private void	checkCoordinate(MappingCoordinate c, int plateCount, PlateGeometryData geometry, boolean destination)	Checks that the coordinate is within the bouds given by the mapping and geometry.
static PlateMapping	getById(DbControl dc, int id)	Get a PlateMapping item when you know the id.
(package private) PlateMappingData	getData()	Get the BasicData object that holds all data for this item.
int	getDestinationCount()	Get the number of produced destination plates.
PlateGeometry	getDestinationGeometry()	Get the PlateGeometry of the created plates.
Date	getEntryDate()	Get the date that the item was registered in the database.
String	getImage()	Get the name of a small image that is a graphical representation of the mapping.
static PlateMapping	getNew(DbControl dc, PlateGeometry sourceGeometry, int sourceCount, PlateGeometry destinationGeometry, int destinationCount)	Create a new PlateMapping item.
static ItemQuery<PlateMapping>	getQuery()	Get a query that returns plate mappings.
MappingCoordinate	getSourceCoordinate(MappingCoordinate destinationCoordinate)	Get the source coordinate for a given destination coordinate.
int	getSourceCount()	Get the number of required source plates.
PlateGeometry	getSourceGeometry()	Get the PlateGeometry that is required for source plates.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: Plate:s created with this mapping
boolean	isUsed()	Check if: A Plate has been created from this mapping
private void	setDestinationCount(int destinationCount)	Set the number of produced destination plates.
private void	setDestinationGeometry(PlateGeometry destinationGeometry)	Set the destination geometry.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setImage(String image)	Set the name of a small image that is a graphical representation of the mapping.
void	setSourceCoordinate(MappingCoordinate destinationCoordinate, MappingCoordinate sourceCoordinate)	Set the source coordinate for a given destination coordinate.
private void	setSourceCount(int sourceCount)	Set the number of source plates.
private void	setSourceGeometry(PlateGeometry sourceGeometry)	Set the source geometry.

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

getDescription, getName, getRemovedBy, isRemoved, setDescription, setName, setRemoved

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

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey

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

getOwner, isOwner, setOwner, takeOwnership

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, isDetached, isInDatabase, onAfterCommit, onAfterInsert, 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

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

getOwner, isOwner, setOwner, takeOwnership

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PLATEMAPPING, getType()

MAX_IMAGE_LENGTH

public static final int MAX_IMAGE_LENGTH

The maximum length of the image name that can be stored in the database. Check the length against this value before calling the setImage(String) method to avoid exceptions.

See Also:

Constant Field Values

Constructor Details

PlateMapping

PlateMapping(PlateMappingData plateMappingData)

Method Details

getNew

public static PlateMapping getNew(DbControl dc,
PlateGeometry sourceGeometry,
int sourceCount,
PlateGeometry destinationGeometry,
int destinationCount)
                           throws PermissionDeniedException,
InvalidDataException,
BaseException

Create a new PlateMapping item.

Parameters:

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

sourceGeometry - The required geometry of the source plates

sourceCount - The number of source plates

destinationGeometry - The geometry of the created destination plates

destinationCount - The number of created destination plates

Returns:

The new PlateMapping item

Throws:

PermissionDeniedException - If the loggged in user doesn't have use permission for the geometries

InvalidDataException - If any of the geometries are null, or any of the count values are less than one

BaseException - If there is another error

getById

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

Get a PlateMapping 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 PlateMapping 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<PlateMapping> getQuery()

Get a query that returns plate mappings.

Returns:

An ItemQuery object

getData

PlateMappingData getData()

Description copied from class: BasicItem

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

Overrides:

getData in class CommonItem

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

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 Plate has been created from this mapping

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:

• Plate:s created with this mapping

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)

getSourceGeometry

public PlateGeometry getSourceGeometry()
                                throws PermissionDeniedException,
BaseException

Get the PlateGeometry that is required for source plates.

Returns:

A PlateGeometry item

Throws:

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

BaseException - If there is another error

setSourceGeometry

private void setSourceGeometry(PlateGeometry sourceGeometry)
                        throws PermissionDeniedException,
InvalidDataException

Set the source geometry.

Throws:

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

InvalidDataException - If the geometry is null

getSourceCount

public int getSourceCount()

Get the number of required source plates.

setSourceCount

private void setSourceCount(int sourceCount)
                     throws InvalidDataException

Set the number of source plates.

Throws:

InvalidDataException - If the source count is less than one

getDestinationGeometry

public PlateGeometry getDestinationGeometry()
                                     throws PermissionDeniedException,
BaseException

Get the PlateGeometry of the created plates.

Returns:

A PlateGeometry item

Throws:

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

BaseException - If there is another error

setDestinationGeometry

private void setDestinationGeometry(PlateGeometry destinationGeometry)
                             throws PermissionDeniedException,
InvalidDataException

Set the destination geometry.

Throws:

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

InvalidDataException - If the geometry is null

getDestinationCount

public int getDestinationCount()

Get the number of produced destination plates.

setDestinationCount

private void setDestinationCount(int destinationCount)
                          throws InvalidDataException

Set the number of produced destination plates.

Throws:

InvalidDataException - If the destination count is less than one

getImage

public String getImage()

Get the name of a small image that is a graphical representation of the mapping.

Returns:

The name of an image or null

setImage

public void setImage(String image)
              throws PermissionDeniedException,
InvalidDataException

Set the name of a small image that is a graphical representation of the mapping. Null is allowed but the value can't be longer than the value specified by the MAX_IMAGE_LENGTH constant.

Parameters:

image - The name of the image

Throws:

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

InvalidDataException - If the value is too long

getSourceCoordinate

public MappingCoordinate getSourceCoordinate(MappingCoordinate destinationCoordinate)

Get the source coordinate for a given destination coordinate.

Parameters:

destinationCoordinate - The destination coordinate

Returns:

A MappingCoordinate object or null if no source coordinate has been specified

setSourceCoordinate

public void setSourceCoordinate(MappingCoordinate destinationCoordinate,
MappingCoordinate sourceCoordinate)
                         throws PermissionDeniedException,
InvalidDataException

Set the source coordinate for a given destination coordinate.

Parameters:

destinationCoordinate - The destination coordinate

sourceCoordinate - The source coordinate, or null to remove the mapping for the destination coordinate

Throws:

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

InvalidDataException - If the destination coordinate is null or any of the coordinates are outside the range of valid coordinates as specified by the geometries

checkCoordinate

private void checkCoordinate(MappingCoordinate c,
int plateCount,
PlateGeometryData geometry,
boolean destination)
                      throws InvalidDataException

Checks that the coordinate is within the bouds given by the mapping and geometry.

Throws:

InvalidDataException

apply

public List<Plate> apply(List<Plate> sourcePlates,
PlateType destinationPlateType)
                  throws PermissionDeniedException,
InvalidDataException,
BaseException

Apply this mapping to the given list of source plates and generate new plates of the specified type. The source plates must all be of the geometry specified by getSourceGeometry() and the destroyed flag mustn't be set. The list must contain exactly the required number of plates as specified by @link #getSourceCount()}. The destination plate type must be of the required destination geometry, getDestinationGeometry().

The new plates are not saved to the database and doesn't have any names, descriptions or other information. It is up to the client application to fill in this information and save the new plates.

Parameters:

sourcePlates - A List containing Plate items

destinationPlateType - The PlateType of the destination plates

Returns:

A List containing the new (unsaved) Plate items

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this plate mapping and to all source plates

InvalidDataException - If any of the parameters are invalid

BaseException - If there is another error