Package net.sf.basedb.core

Class DataCubeLayer

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.DataCubeLayer

All Implemented Interfaces:

AccessControlled, Identifiable

public class DataCubeLayer
extends ChildItem

This represents the layer coordinate in a data cube. A BioAssaySet must have a link to an item of this type. It is possible for more than one bioassayset to link to the same layer. This item keeps track of two important things. The layer coordinate number and the number of bytes the data in this layer occupies on disk. The number of bytes is reported up to the Experiment which is the item that handles user quota.

Version:

2.0

Author:

Nicklas

See Also:

• DataCube
• BioAssaySet.getDataCubeLayer()
• BioAssaySet.getDataCubeLayerNo()

Last modified

$Date: 2015-04-17 14:02:22 +0200 (fr, 17 apr 2015) $

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
DataCubeLayer(DataCubeLayerData data)	Creates a new data cube item from the given data.

Method Summary

Modifier and Type	Method	Description
(package private) void	addBytes(long bytes)
static DataCubeLayer	getById(DbControl dc, int id)	Get a DataCubeLayer item when you know the id.
long	getBytes()	Get the number of bytes the data stored in this layer occupies on disk.
(package private) DataCubeLayerData	getData()	Get the BasicData object that holds all data for this item.
DataCube	getDataCube()	Get the data cube this layer belongs to.
short	getDataCubeNo()	Get the number of the data cube this layer belongs to.
short	getLayerNo()	Get the number of this layer.
(package private) static DataCubeLayer	getNew(DbControl dc, DataCube cube)	Create a new DataCubeLayer item.
(package private) Permission	getPermissionForWriteDeleteAndCreate()	USE permission is enough to be able to manage data cubes.
(package private) SharedData	getSharedParent()	Get the experiment.
Item	getType()	Get the type of item represented by the object.
(package private) VirtualDb	getVirtualDb()	Get the virtual database this layer belongs to.
(package private) void	onBeforeCommit(Transactional.Action action)	Delete data and update disk usage information on the experiment if action == Action.DELETE
private void	setDataCube(DataCube cube)	Set the data cube.
private void	setLayerNo(short layerNo)

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

getPermissionForUse, getPluginPermissions, initPermissions

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

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

Methods inherited from class java.lang.Object

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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.DATACUBELAYER
• getType()

Constructor Details

DataCubeLayer

DataCubeLayer(DataCubeLayerData data)

Creates a new data cube item from the given data.

Parameters:

data - the data

Method Details

getNew

static DataCubeLayer getNew(DbControl dc,
 DataCube cube)
                     throws BaseException

Create a new DataCubeLayer item.

Parameters:

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

cube - The cube the new layer is located in

Returns:

The new DataCubeLayer item

Throws:

BaseException - If there is an error

getById

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

Get a DataCubeLayer 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 DataCubeLayer 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

getData

DataCubeLayerData 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.

Returns:

A value indicating the type of item

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
             throws BaseException

Delete data and update disk usage information on the experiment if action == Action.DELETE

Overrides:

onBeforeCommit in class BasicItem

Throws:

BaseException - If there is an error

See Also:

• Transactional
• Developer documentation: Transactions
• Developer documentation: Coding rules and guidelines for item classes

getSharedParent

SharedData getSharedParent()

Get the experiment.

Specified by:

getSharedParent in class ChildItem

Returns:

The parent item

getPermissionForWriteDeleteAndCreate

Permission getPermissionForWriteDeleteAndCreate()

USE permission is enough to be able to manage data cubes.

Overrides:

getPermissionForWriteDeleteAndCreate in class ChildItem

getDataCube

public DataCube getDataCube()
                     throws PermissionDeniedException,
BaseException

Get the data cube this layer belongs to.

Returns:

A DataCube object

Throws:

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

BaseException - If there is another error

setDataCube

private void setDataCube(DataCube cube)

Set the data cube. This cannot be changed after the filter has been created.

getDataCubeNo

public short getDataCubeNo()

Get the number of the data cube this layer belongs to.

getLayerNo

public short getLayerNo()

Get the number of this layer.

setLayerNo

private void setLayerNo(short layerNo)

getBytes

public long getBytes()

Get the number of bytes the data stored in this layer occupies on disk.

addBytes

void addBytes(long bytes)

getVirtualDb

VirtualDb getVirtualDb()

Get the virtual database this layer belongs to.