Package net.sf.basedb.core

Class DataCubeFilter

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.DataCubeFilter

All Implemented Interfaces:

AccessControlled, Identifiable

public class DataCubeFilter
extends ChildItem

This represents a filter in a datacube. A filter simply contains a set of column/position coordinates of spots that has passed som filtering criteria. In theory a filter can be used on any layer in the data cube, but in practice filters are not reused among bioassaysets with different layers. This item keeps track of two important things. The filter 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
• FilterBatcher

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
DataCubeFilter(DataCubeFilterData 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 DataCubeFilter	getById(DbControl dc, int id)	Get a DataCubeFilter item when you know the id.
long	getBytes()	Get the number of bytes the data stored in this filter occupies on disk.
(package private) DataCubeFilterData	getData()	Get the BasicData object that holds all data for this item.
DataCube	getDataCube()	Get the data cube this filter belongs to.
short	getDataCubeNo()	Get the number of the data cube this filter belongs to.
short	getFilterNo()	Get the number of this filter.
(package private) static DataCubeFilter	getNew(DbControl dc, DataCube cube)	Create a new DataCubeFilter 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 filter 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	setFilterNo(short filterNo)

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.DATACUBEFILTER
• getType()

Constructor Details

DataCubeFilter

DataCubeFilter(DataCubeFilterData data)

Creates a new data cube item from the given data.

Parameters:

data - the data

Method Details

getNew

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

Create a new DataCubeFilter item.

Parameters:

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

cube - The cube the new filter is located in

Returns:

The new DataCubeFilter item

Throws:

BaseException - If there is an error

getById

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

Get a DataCubeFilter 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 DataCubeFilter 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

DataCubeFilterData 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 filter 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 filter belongs to.

getFilterNo

public short getFilterNo()

Get the number of this filter.

setFilterNo

private void setFilterNo(short filterNo)

getBytes

public long getBytes()

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

addBytes

void addBytes(long bytes)

getVirtualDb

VirtualDb getVirtualDb()

Get the virtual database this filter belongs to.