Package net.sf.basedb.core

Class BioAssay

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.BioAssay

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable

public class BioAssay
extends ChildItem
implements Nameable, Annotatable

Represents the current intensities of raw data after some transformation has been applied to it. Usually a single bioassay represents the data from a single RawBioAssay but it is also possible that a transformation has merged several bioassays into a single one.

Bioassays are created by one of the BioAssaySet.newRootBioAssay(Collection), BioAssaySet.newBioAssay(BioAssay) or BioAssaySet.newBioAssay(Collection). Which one to use depends on the relationship to it's parents. Bioassays can only be created if the bioassayset hasn't been committed to the database.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2005-10-19 15:57:12 +0200 (on, 19 okt 2005) $

Field Summary

Fields

Modifier and Type	Field	Description
static final 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
BioAssay(BioAssayData data)	Creates a new bioassay item from the given data.

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get the parent bioassay set, all parent bioassays and all parent root raw bioassays.
AnnotationSet	getAnnotationSet()	Get the annotation set containing the annotations for this item.
BioAssaySet	getBioAssaySet()	Get the bioassayset this bioassay belongs to.
static BioAssay	getById(DbControl dc, int id)	Get a BioAssay item when you know the id.
(package private) BioAssayData	getData()	Get the BasicData object that holds all data for this item.
(package private) DataCubeColumn	getDataCubeColumn()	Get the DataCubeColumn object where this bioassay store it's data.
short	getDataCubeColumnNo()	Get the column coordinate in the data cube that this bioassay stores it's data in.
short	getDataCubeLayerNo()	Get the layer coordinate in the data cube that this bioassay stores it's data in.
short	getDataCubeNo()	Get the number of the data cube this bioassay stores it's data in.
String	getDescription()	Get the description for the item.
Experiment	getExperiment()	Get the experiment this bioassay belongs to.
String	getName()	Get the name of the item.
(package private) static BioAssay	getNew(DbControl dc, BioAssaySet bioAssaySet, DataCubeColumn column)	Create a new BioAssay item.
int	getNumFileSpots()	Get the number of spots that are stored in files.
int	getNumSpots()	Get the number of spots in this bioassay.
ItemQuery<BioAssay>	getParents()	Get a query for loading the parents bioassays to this bioassay.
(package private) Permission	getPermissionForWriteDeleteAndCreate()	USE permission is enough to be able to manage bioassays.
Protocol	getProtocol()	Default implementation returns null.
static ItemQuery<BioAssay>	getQuery(BioAssaySet bioAssaySet)	Get a query configured to retrieve bioassays in a given bioassayset.
ItemQuery<RawBioAssay>	getRawBioAssays()
RawDataType	getRawDataType()	Get the raw data type the experiment uses for the raw data.
ItemQuery<RootRawBioAssay>	getRootRawBioAssays()
(package private) SharedData	getSharedParent()	Get the experiment.
DynamicSpotQuery	getSpotData()	Get a query that returns spot data for this bioassay.
Item	getType()	Get the type of item represented by the object.
(package private) void	initPermissions(int granted, int denied)	Deny DELETE permission.
boolean	isAnnotated()	Check if this item has an annotation set.
(package private) void	onBeforeCommit(Transactional.Action action)	This method is called on each Transactional item and on all items if the action is Transactional.Action.CREATE or Transactional.Action.DELETE before a commit is issued to the database.
void	removeAnnotations()	Remove all annotations from this item, by deleting the annotation set.
private void	setBioAssaySet(BioAssaySet bioAssaySet)	Set the experiment.
private void	setDataCubeColumn(DataCubeColumn column)
void	setDescription(String description)	Set the description for the item.
void	setName(String name)	Set the name of the item.
void	setNumFileSpots(int numSpots)	Set the number of spots that are stored in files.

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, 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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.BIOASSAY
• getType()

Constructor Details

BioAssay

BioAssay(BioAssayData data)

Creates a new bioassay item from the given data.

Parameters:

data - the data

Method Details

getNew

static BioAssay getNew(DbControl dc,
 BioAssaySet bioAssaySet,
 DataCubeColumn column)
                throws PermissionDeniedException,
InvalidDataException,
BaseException

Create a new BioAssay item.

Parameters:

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

bioAssaySet - The bioassayset the bioassay belongs to

column - The data cube column where the bioassay should store it's data; must be unique among bioassays in a bioassayset

Returns:

The new BioAssay item

Throws:

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

InvalidDataException - If the bioassayset is null

BaseException - If there is an error

getById

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

Get a BioAssay 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 BioAssay 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<BioAssay> getQuery(BioAssaySet bioAssaySet)
                                    throws InvalidDataException

Get a query configured to retrieve bioassays in a given bioassayset.

Parameters:

bioAssaySet - The bioassayset to retreive bioassays for, null is not allowed

Returns:

An ItemQuery object

Throws:

InvalidDataException - If the parameter is null.

getData

BioAssayData 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.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

getName

public String getName()

Description copied from interface: Nameable

Get the name of the item.

Specified by:

getName in interface Nameable

Returns:

A String with the name of the item

setName

public void setName(String name)
             throws PermissionDeniedException,
InvalidDataException

Description copied from interface: Nameable

Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the Nameable.MAX_NAME_LENGTH constant.

Specified by:

setName in interface Nameable

Parameters:

name - The new name for the item

Throws:

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

InvalidDataException - If the name is null or longer than specified by the Nameable.MAX_NAME_LENGTH constant

getDescription

public String getDescription()

Description copied from interface: Nameable

Get the description for the item.

Specified by:

getDescription in interface Nameable

Returns:

A String with a description of the item

setDescription

public void setDescription(String description)
                    throws PermissionDeniedException,
InvalidDataException

Description copied from interface: Nameable

Set the description for the item. The description can be null but mustn't be longer than the value specified by the Nameable.MAX_DESCRIPTION_LENGTH constant.

Specified by:

setDescription in interface Nameable

Parameters:

description - The new description for the item

Throws:

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

InvalidDataException - If the description longer than specified by the Nameable.MAX_DESCRIPTION_LENGTH constant

getAnnotationSet

public AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Get the annotation set containing the annotations for this item. If the item doesn't have any annotations a new annotation set is created and automatically saved to the database when DbControl.commit() is called. To check if an item has annotations without creating a new annotation set use the Annotatable.isAnnotated() method.

Specified by:

getAnnotationSet in interface Annotatable

Returns:

An AnnotationSet

Throws:

PermissionDeniedException - If the logged in user doesn't have enough permissions

BaseException - If there is another error

Since:

2.2

isAnnotated

public boolean isAnnotated()

Description copied from interface: Annotatable

Check if this item has an annotation set. The annotation set may be empty.

Specified by:

isAnnotated in interface Annotatable

Returns:

TRUE if an annotation set exists, FALSE otherwise

Since:

2.2

removeAnnotations

public void removeAnnotations()
                       throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Remove all annotations from this item, by deleting the annotation set.

Specified by:

removeAnnotations in interface Annotatable

Throws:

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

BaseException - If there is another error

Since:

2.2

getProtocol

public Protocol getProtocol()

Default implementation returns null. Should be overriden by subclasses that has protocols.

Specified by:

getProtocol in interface Annotatable

Returns:

Always null

Since:

2.2

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the parent bioassay set, all parent bioassays and all parent root raw bioassays.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

Since:

2.2

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
             throws BaseException

Description copied from class: BasicItem

This method is called on each Transactional item and on all items if the action is Transactional.Action.CREATE or Transactional.Action.DELETE before a commit is issued to the database. If the subclass overrides this method it must also propagate the call to the superclass, ie. super.onBeforeCommit(action).

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

initPermissions

void initPermissions(int granted,
 int denied)
              throws BaseException

Deny DELETE permission. BioAssays are automatically deleted when it's parent bioassayset is deleted.

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 bioassays.

Overrides:

getPermissionForWriteDeleteAndCreate in class ChildItem

getExperiment

public Experiment getExperiment()
                         throws PermissionDeniedException,
BaseException

Get the experiment this bioassay belongs to.

Returns:

An Experiment object

Throws:

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

BaseException - If there is another error

getBioAssaySet

public BioAssaySet getBioAssaySet()
                           throws PermissionDeniedException,
BaseException

Get the bioassayset this bioassay belongs to.

Returns:

A BioAssaySet object

Throws:

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

BaseException - If there is another error

setBioAssaySet

private void setBioAssaySet(BioAssaySet bioAssaySet)
                     throws PermissionDeniedException,
InvalidDataException

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

Throws:

PermissionDeniedException

InvalidDataException

getRawDataType

public RawDataType getRawDataType()

Get the raw data type the experiment uses for the raw data.

Returns:

A RawDataType object

getNumSpots

public int getNumSpots()

Get the number of spots in this bioassay.

getNumFileSpots

public int getNumFileSpots()

Get the number of spots that are stored in files.

Since:

2.8

setNumFileSpots

public void setNumFileSpots(int numSpots)

Set the number of spots that are stored in files.

Parameters:

numSpots - The number of spots

Since:

2.8

getDataCubeNo

public short getDataCubeNo()

Get the number of the data cube this bioassay stores it's data in.

See Also:

• getDataCubeLayerNo()
• getDataCubeColumnNo()

getDataCubeLayerNo

public short getDataCubeLayerNo()

Get the layer coordinate in the data cube that this bioassay stores it's data in.

See Also:

• getDataCubeNo()
• getDataCubeColumnNo()

getDataCubeColumnNo

public short getDataCubeColumnNo()

Get the column coordinate in the data cube that this bioassay stores it's data in.

See Also:

• getDataCubeNo()
• getDataCubeLayerNo()

getDataCubeColumn

DataCubeColumn getDataCubeColumn()
                          throws PermissionDeniedException,
BaseException

Get the DataCubeColumn object where this bioassay store it's data.

Throws:

PermissionDeniedException

BaseException

setDataCubeColumn

private void setDataCubeColumn(DataCubeColumn column)

getSpotData

public DynamicSpotQuery getSpotData()

Get a query that returns spot data for this bioassay. The query will select column, position and spot intensities by default. This method uses the BioAssaySet.getSpotData() method and adds a restriction to the returned query.

Returns:

A DynamicSpotQuery object

See Also:

• BioAssaySet.getSpotData()

getParents

public ItemQuery<BioAssay> getParents()

Get a query for loading the parents bioassays to this bioassay. If this bioassay belong to a root bioassayset, null is returned.

Returns:

A query returning the parent bioassays of this bioassay, or null

getRawBioAssays

public ItemQuery<RawBioAssay> getRawBioAssays()

Returns:

A query returning the raw bioassays this bioassay is created from

getRootRawBioAssays

public ItemQuery<RootRawBioAssay> getRootRawBioAssays()

Returns:

A query returning the root raw bioassays this bioassay is created from

Since:

3.6