Package net.sf.basedb.core

Class ExtraValue

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.ExtraValue

All Implemented Interfaces:

AccessControlled, FileStoreEnabled, Identifiable

public class ExtraValue
extends ChildItem
implements FileStoreEnabled

Represents extra values attached to a BioAssaySet. The type of extra values are defined by the ExtraValueType. The insertion of extra values is done using batchers, created by calling either BioAssaySet.getSpotExtraValueBatcher(Class, ExtraValueType, Job) or BioAssaySet.getPositionExtraValueBatcher(Class, ExtraValueType, Job). Only one set of extra values of the same ExtraValueType are allowed in a bioassayset.

Version:

2.0

Author:

Nicklas

See Also:

• SpotExtraValueBatcher
• PositionExtraValueBatcher

Last modified

$Date: 2015-04-21 09:59:42 +0200 (ti, 21 apr 2015) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ExtraValue.CoordinateType	Defines which coordinates in the data cube the extra values are attached to.

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
ExtraValue(ExtraValueData data)	Creates a new extra value item from the given data.

Method Summary

Modifier and Type	Method	Description
BioAssaySet	getBioAssaySet()	Get the bioassayset this extra value belongs to.
static ExtraValue	getById(DbControl dc, int id)	Get an ExtraValue item when you know the id.
ExtraValue.CoordinateType	getCoordinateType()	Get information about which coordinates in the data cube the extra values are attached to.
(package private) ExtraValueData	getData()	Get the BasicData object that holds all data for this item.
(package private) DataCube	getDataCube()
(package private) DataCubeExtraValue	getDataCubeExtraValue()
short	getDataCubeNo()	Get the number of the data cube the extra values are stored in.
Experiment	getExperiment()	Get the experiment this extra value belongs to.
short	getExtraNo()	Get the number in the data cube of the extra values.
ExtraValueType	getExtraValueType()	Get the type of the extra values.
FileSet	getFileSet()	Get the file set that collects all files that holds data for this item.
Job	getJob()	Get the job that created the extra values.
(package private) String	getJoinAlias()	The alias used when joining this extra value into a query.
(package private) static ExtraValue	getNew(DbControl dc, BioAssaySet bioAssaySet, ExtraValueType extraValueType, DataCubeExtraValue dcev, Job job)	Create a new ExtraValue item.
int	getNumFileValues()	Get the number of values that are stored in files.
int	getNumValues()	Get the number of extra values inserted.
Collection<FileSet>	getParentFileSets()	Get the file set from the parent bioassay set if it exists.
(package private) Permission	getPermissionForWriteDeleteAndCreate()	USE permission is enough to be able to manage extra values.
Platform	getPlatform()	Get the platform the item is related to.
static ItemQuery<ExtraValue>	getQuery(BioAssaySet bioAssaySet)	Get a query configured to retrieve extra values in a given bioassayset.
RawDataType	getRawDataType()	Get the raw data type the experiment uses for the raw data.
(package private) SharedData	getSharedParent()	Get the experiment.
Item	getType()	Get the type of item represented by the object.
DynamicExtraValueQuery	getValues()	Get a query returning the extra values.
Type	getValueType()	Get the type of values.
PlatformVariant	getVariant()	Get the platform variant the item is related to.
VirtualColumn	getVirtualColumn()	Get the virtual column object that represents the column where the extra values are stored.
(package private) VirtualDb	getVirtualDb()
(package private) VirtualTable	getVirtualTable()
boolean	hasFileSet()	Check if this item has a file set.
private void	setBioAssaySet(BioAssaySet bioAssaySet)	Set the bioassayset.
private void	setDataCubeExtraValue(DataCubeExtraValue dcev)
private void	setExtraValueType(ExtraValueType extraValueType)	Set the extra value type.
private void	setJob(Job job)	Set the job that created the extra values.
void	setNumFileValues(int numValues)	Set the number of extra values that are stored in files.
(package private) void	setNumValues(int numValues)	Called from batcher when it is closed.

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, onBeforeCommit, 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.EXTRAVALUE
• getType()

Constructor Details

ExtraValue

ExtraValue(ExtraValueData data)

Creates a new extra value item from the given data.

Parameters:

data - the data

Method Details

getNew

static ExtraValue getNew(DbControl dc,
 BioAssaySet bioAssaySet,
 ExtraValueType extraValueType,
 DataCubeExtraValue dcev,
 Job job)
                  throws PermissionDeniedException,
InvalidDataException,
BaseException

Create a new ExtraValue item.

Parameters:

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

bioAssaySet - The bioassayset the extra value belongs to

extraValueType - The type of the extra value

dcev - The data cube extra value used to store the extra values

job - The job that calculated the extra values or null

Returns:

The new ExtraValue item

Throws:

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

InvalidDataException - If the bioassayset or extra value type is null

BaseException - If there is an error

getById

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

Get an ExtraValue 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 ExtraValue 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<ExtraValue> getQuery(BioAssaySet bioAssaySet)
                                      throws InvalidDataException

Get a query configured to retrieve extra values in a given bioassayset.

Parameters:

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

Returns:

An ItemQuery object

Throws:

InvalidDataException - If the argument is null.

See Also:

• getValues()

getData

ExtraValueData 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

getFileSet

public FileSet getFileSet()

Description copied from interface: FileStoreEnabled

Get the file set that collects all files that holds data for this item. If no file set exists a new one is created and automatically saved to the database when DbControl.commit() is called. To check if an item has files without creating a new file set use the FileStoreEnabled.hasFileSet() method.

Specified by:

getFileSet in interface FileStoreEnabled

Returns:

A file set

Since:

2.8

hasFileSet

public boolean hasFileSet()

Description copied from interface: FileStoreEnabled

Check if this item has a file set. Always call this method before FileStoreEnabled.getFileSet() to avoid creating a new file set when there is no need for it.

Specified by:

hasFileSet in interface FileStoreEnabled

Returns:

TRUE if a file set exists, FALSE if not

Since:

2.8

getPlatform

public Platform getPlatform()

Description copied from interface: FileStoreEnabled

Get the platform the item is related to. The platform is used to limit the DataFileType:s that can be added to the file set.

Specified by:

getPlatform in interface FileStoreEnabled

Returns:

Always null

Since:

2.8

getVariant

public PlatformVariant getVariant()

Description copied from interface: FileStoreEnabled

Get the platform variant the item is related to. The platform is used to limit the DataFileType:s that can be added to the file set.

Specified by:

getVariant in interface FileStoreEnabled

Returns:

Always null

Since:

2.8

getParentFileSets

public Collection<FileSet> getParentFileSets()

Get the file set from the parent bioassay set if it exists.

Specified by:

getParentFileSets in interface FileStoreEnabled

Returns:

A collection of FileSet or null

Since:

2.8

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 extra values.

Overrides:

getPermissionForWriteDeleteAndCreate in class ChildItem

getExperiment

public Experiment getExperiment()
                         throws PermissionDeniedException,
BaseException

Get the experiment this extra value 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 extra value 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 bioassayset. This cannot be changed after the extra value has been created.

Throws:

PermissionDeniedException

InvalidDataException

getExtraValueType

public ExtraValueType getExtraValueType()
                                 throws PermissionDeniedException,
BaseException

Get the type of the extra values.

Returns:

An ExtraValueType object

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the extra value type

BaseException - If there is another error

setExtraValueType

private void setExtraValueType(ExtraValueType extraValueType)
                        throws PermissionDeniedException,
InvalidDataException

Set the extra value type. This cannot be changed after the extra value has been created.

Throws:

PermissionDeniedException

InvalidDataException

getJob

public Job getJob()
           throws PermissionDeniedException,
BaseException

Get the job that created the extra values.

Returns:

A Job object, ot null if the extra values wasn't created by a job

Throws:

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

BaseException - If there is another error

setJob

private void setJob(Job job)

Set the job that created the extra values. Once set it can't be changed.

getRawDataType

public RawDataType getRawDataType()

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

Returns:

A RawDataType object

getNumValues

public int getNumValues()

Get the number of extra values inserted.

setNumValues

void setNumValues(int numValues)

Called from batcher when it is closed.

getNumFileValues

public int getNumFileValues()

Get the number of values that are stored in files.

Since:

2.8

setNumFileValues

public void setNumFileValues(int numValues)

Set the number of extra values that are stored in files.

Parameters:

numValues - The number of spots

Since:

2.8

getDataCubeNo

public short getDataCubeNo()

Get the number of the data cube the extra values are stored in.

getExtraNo

public short getExtraNo()

Get the number in the data cube of the extra values.

getCoordinateType

public ExtraValue.CoordinateType getCoordinateType()

Get information about which coordinates in the data cube the extra values are attached to.

Returns:

A CoordinateType object

See Also:

• DataCube

getValueType

public Type getValueType()

Get the type of values. Shortcut for getExtraValueType().getValueType().

Returns:

A Type object

getValues

public DynamicExtraValueQuery getValues()

Get a query returning the extra values. The query will select column, position and the extra value by default, if the extra values attached to both column and position. Otherwise only the coordinate the extra values are attached to are selected.

// Example of default query for extra integer values attached to spots
SELECT ex.column, ex.position, ex.value
FROM Dynamic#SpotExtraInt AS ex
WHERE ex.cube = <cube_no> AND ex.extra = <extra_no>

Returns:

A DynamicExtraValueQuery object

getDataCubeExtraValue

DataCubeExtraValue getDataCubeExtraValue()
                                  throws PermissionDeniedException,
BaseException

Throws:

PermissionDeniedException

BaseException

setDataCubeExtraValue

private void setDataCubeExtraValue(DataCubeExtraValue dcev)

getVirtualDb

VirtualDb getVirtualDb()

getDataCube

DataCube getDataCube()

getVirtualTable

VirtualTable getVirtualTable()

getVirtualColumn

public VirtualColumn getVirtualColumn()

Get the virtual column object that represents the column where the extra values are stored. The column depends on the value type of the extra value.

Returns:

A VirtualColumn object

See Also:

• VirtualColumn.extraValue(Type)

getJoinAlias

String getJoinAlias()

The alias used when joining this extra value into a query. We can't use the VirtualTable.getAlias() value, which we normally do, since the alias must be unique if we join several extra values. We simply return a value based on the id of this item. The ExtraValueJoin and ExtraValueExpression both uses this method to create their SQL.

Returns:

The alias to use in joins

See Also:

• ExtraValueJoin
• ExtraValueExpression