Package net.sf.basedb.core

Class DataCubeColumn

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.DataCubeColumn

All Implemented Interfaces:

AccessControlled, Identifiable

public class DataCubeColumn
extends ChildItem

Represents the column coordinate in a data cube. A BioAssay must have a link to an item of this type. It is possible for more than one bioassay to link to the same column. Actually, if two BioAssaySet:s, one which is the child of the other, are in the same data cube, a bioassay must link to the same column as the parent bioassay.

Version:

2.0

Author:

Nicklas

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
DataCubeColumn(DataCubeColumnData data)	Creates a new data cube item from the given data.

Method Summary

Modifier and Type	Method	Description
static DataCubeColumn	getById(DbControl dc, int id)	Get a DataCubeColumn item when you know the id.
short	getColumnNo()	Get the number of this column.
(package private) DataCubeColumnData	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.
(package private) static DataCubeColumn	getNew(DbControl dc, DataCube cube)	Create a new DataCubeColumn 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 column belongs to.
(package private) void	initPermissions(int granted, int denied)	Deny DELETE permission.
private void	setColumnNo(short columnNo)
private void	setDataCube(DataCube cube)	Set the experiment.

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

getPermissionForUse, getPluginPermissions

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, onBeforeCommit, 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.DATACUBECOLUMN
• getType()

Constructor Details

DataCubeColumn

DataCubeColumn(DataCubeColumnData data)

Creates a new data cube item from the given data.

Parameters:

data - the data

Method Details

getNew

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

Create a new DataCubeColumn item.

Parameters:

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

cube - The cube the new column is located in

Returns:

The new DataCubeColumn item

Throws:

BaseException - If there is an error

getById

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

Get a DataCubeColumn 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 DataCubeColumn 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

DataCubeColumnData 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

initPermissions

void initPermissions(int granted,
 int denied)
              throws BaseException

Deny DELETE permission. Columns are automatically deleted when the data cube is deleted (by Hibernate cascade).

Overrides:

initPermissions in class ChildItem

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

Throws:

BaseException - If the permissions couldn't be initialised

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)
                  throws PermissionDeniedException,
InvalidDataException

Set the experiment. This cannot be changed after the dynamic tables has been created.

Throws:

PermissionDeniedException

InvalidDataException

getDataCubeNo

public short getDataCubeNo()

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

getColumnNo

public short getColumnNo()

Get the number of this column.

setColumnNo

private void setColumnNo(short columnNo)

getVirtualDb

VirtualDb getVirtualDb()

Get the virtual database this column belongs to.