Package net.sf.basedb.core

Class ArrayDesignBlock

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.ArrayDesignBlock

All Implemented Interfaces:

AccessControlled, Identifiable

public class ArrayDesignBlock
extends ChildItem

Version:

2.0

Author:

Enell

Last modified

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

Field Summary

Fields

Modifier and Type	Field	Description
static Item	TYPE	The type of item represented by this class.

Constructor Summary

Constructors

Constructor	Description
ArrayDesignBlock(ArrayDesignBlockData data)

Method Summary

Modifier and Type	Method	Description
ArrayDesign	getArrayDesign()	Get the ArrayDesign that is linked with this block.
int	getBlockNumber()	Get the block number of this block.
int	getBlockSizeX()	Get the number of columns in this block.
int	getBlockSizeY()	Get the number of rows in this block.
static ArrayDesignBlock	getById(DbControl dc, int id)	Get a ArrayDesignBlock object when you know the ID.
(package private) ArrayDesignBlockData	getData()	Get the BasicData object that holds all data for this item.
int	getFeatureDiameter()	Get the expected diameter of spots on the slide.
int	getMetaGridX()	Get the column coordinate of this block.
int	getMetaGridY()	Get the row coordinate of this block.
(package private) static ArrayDesignBlock	getNew(DbControl dc, ArrayDesign arrayDesign, BlockInfo blockInfo)
int	getOriginX()	Get the distance from the left edge of the slide to the top left spot in the block.
int	getOriginY()	Get the distance from the top edge of the slide to the top left spot in the block.
static ItemQuery<ArrayDesignBlock>	getQuery(ArrayDesign arrayDesign)	Get a query configured to retrieve array design blocks for the specified array design.
(package private) SharedData	getSharedParent()	Get the shareable parent item of this child item.
int	getSpacingX()	Get the x spacing between the spots in the slide.
int	getSpacingY()	Get the y spacing between the spots in the slide.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get the array design this block is a part of.
boolean	hasFeatures()	Checks if this ArrayDesignBlock has any features.
(package private) void	initPermissions(int granted, int denied)	WRITE and DELETE permissions are always denied.
boolean	isUsed()	Array design blocks are always used by an array design.
private void	setArrayDesign(ArrayDesign arrayDesign)	Set the ArrayDesign for this block.
private void	setBlockNumber(int blockNumber)	Set the block number of this block.
void	setBlockSizeX(int blockSizeX)	Set the number of columns in this block.
void	setBlockSizeY(int blockSizeY)	Set the number of rows in this block.
void	setFeatureDiameter(int diameter)	Set the expected diameter of spots on the slide.
private void	setMetaGrid(int metaGridX, int metaGridY)	Set the metagrid coordinates.
void	setOriginX(int originX)	Set the distance from the left edge of the slide to the top left spot in this block.
void	setOriginY(int originY)	Set the distance from the top edge of the slide to the top left spot in this block.
void	setSpacingX(int spacingX)	Set the x spacing between the spots in the slide.
void	setSpacingY(int spacingY)	Set the y spacing between the spots in the slide.

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

getPermissionForUse, getPermissionForWriteDeleteAndCreate, getPluginPermissions

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, 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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.ARRAYDESIGNBLOCK, getType()

Constructor Details

ArrayDesignBlock

ArrayDesignBlock(ArrayDesignBlockData data)

Method Details

getNew

static ArrayDesignBlock getNew(DbControl dc,
ArrayDesign arrayDesign,
BlockInfo blockInfo)
                        throws BaseException

Throws:

BaseException

getById

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

Get a ArrayDesignBlock object 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 ArrayDesignBlock item

Throws:

ItemNotFoundException - If an item with the specified ID is not found

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

BaseException - If there is another error

getQuery

public static ItemQuery<ArrayDesignBlock> getQuery(ArrayDesign arrayDesign)

Get a query configured to retrieve array design blocks for the specified array design.

Parameters:

arrayDesign - The array design to retreive blocks for, null is not allowed

Returns:

An ItemQuery object

getData

ArrayDesignBlockData 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

isUsed

public boolean isUsed()
               throws BaseException

Array design blocks are always used by an array design.

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()
                             throws BaseException

Get the array design this block is a part of.

Overrides:

getUsingItems in class BasicItem

Returns:

A set containing proxies for the items, or an empty set if no items are using this item

Throws:

BaseException - If there is an error loading the items

Since:

2.2

See Also:

BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)

initPermissions

void initPermissions(int granted,
int denied)
              throws BaseException

WRITE and DELETE permissions are always denied.

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()

Description copied from class: ChildItem

Get the shareable parent item of this child item. This is used by the ChildItem.initPermissions(int, int) method to calculate the logged in user's permissions for the child item.

Specified by:

getSharedParent in class ChildItem

Returns:

The parent item

getArrayDesign

public ArrayDesign getArrayDesign()
                           throws PermissionDeniedException,
BaseException

Get the ArrayDesign that is linked with this block.

Returns:

An ArrayDesign item

Throws:

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

BaseException - This exception is thrown if there is another error

setArrayDesign

private void setArrayDesign(ArrayDesign arrayDesign)
                     throws InvalidDataException

Set the ArrayDesign for this block.

Throws:

InvalidDataException

getMetaGridX

public int getMetaGridX()

Get the column coordinate of this block.

Returns:

the column coordinate

getMetaGridY

public int getMetaGridY()

Get the row coordinate of this block.

Returns:

the row coordinate

setMetaGrid

private void setMetaGrid(int metaGridX,
int metaGridY)
                  throws InvalidDataException

Set the metagrid coordinates. If the coordinates are unknown the both should be set to 0 otherwise the coordinates must be greater then 0.

Parameters:

metaGridX - the column coordinate

Throws:

InvalidDataException

getBlockNumber

public int getBlockNumber()

Get the block number of this block.

Returns:

The number of this block.

setBlockNumber

private void setBlockNumber(int blockNumber)
                     throws InvalidDataException

Set the block number of this block.

Parameters:

blockNumber - the block number of this block

Throws:

InvalidDataException - if the blocknumber is less then 1

getBlockSizeX

public int getBlockSizeX()

Get the number of columns in this block.

Returns:

the number of columns in this block.

setBlockSizeX

public void setBlockSizeX(int blockSizeX)
                   throws InvalidDataException

Set the number of columns in this block. Must be greater then 0.

Parameters:

blockSizeX - the number of rows in this block.

Throws:

InvalidDataException - if blockSizeX is less then 1

getBlockSizeY

public int getBlockSizeY()

Get the number of rows in this block.

Returns:

the number of rows in this block

setBlockSizeY

public void setBlockSizeY(int blockSizeY)
                   throws InvalidDataException

Set the number of rows in this block. Must be greater then 0.

Parameters:

blockSizeY - the number of columns in this block.

Throws:

InvalidDataException - if blockSizeY is less then 1

getOriginX

public int getOriginX()

Get the distance from the left edge of the slide to the top left spot in the block.

Returns:

the distance from the edge

setOriginX

public void setOriginX(int originX)
                throws InvalidDataException

Set the distance from the left edge of the slide to the top left spot in this block.

Parameters:

originX - the distance from the edge

Throws:

InvalidDataException - if originX is less then 0

getOriginY

public int getOriginY()

Get the distance from the top edge of the slide to the top left spot in the block.

Returns:

the distance from the edge

setOriginY

public void setOriginY(int originY)
                throws InvalidDataException

Set the distance from the top edge of the slide to the top left spot in this block.

Parameters:

originY - the distance from the edge

Throws:

InvalidDataException - if originY is less then 0

getSpacingX

public int getSpacingX()

Get the x spacing between the spots in the slide.

Returns:

the spacing between the spots

setSpacingX

public void setSpacingX(int spacingX)
                 throws InvalidDataException

Set the x spacing between the spots in the slide.

Parameters:

spacingX - the spacing between the spots

Throws:

InvalidDataException - if spacingX is less then 0

getSpacingY

public int getSpacingY()

Get the y spacing between the spots in the slide.

Returns:

the spacing between the spots

setSpacingY

public void setSpacingY(int spacingY)
                 throws InvalidDataException

Set the y spacing between the spots in the slide.

Parameters:

spacingY - the spacing between the spots

Throws:

InvalidDataException - if spacingY is less then 0

getFeatureDiameter

public int getFeatureDiameter()

Get the expected diameter of spots on the slide.

Returns:

The expected diameter.

Since:

2.7

setFeatureDiameter

public void setFeatureDiameter(int diameter)
                        throws InvalidDataException

Set the expected diameter of spots on the slide.

Parameters:

diameter - The expected diameter

Throws:

InvalidDataException - If the diameter is less then 0

hasFeatures

public boolean hasFeatures()

Checks if this ArrayDesignBlock has any features.

Returns:

TRUE if the AraryDesignBlock has any fetures