net.sf.basedb.core
Class BioAssaySet

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.ChildItem<BioAssaySetData>
          net.sf.basedb.core.BioAssaySet

All Implemented Interfaces:

AccessControlled, Annotatable, FileStoreEnabled, Identifiable, Nameable, Removable, ToTransferable<BioAssaySetInfo>

public class BioAssaySet
extends ChildItem<BioAssaySetData>
implements Nameable, Removable, Annotatable, FileStoreEnabled, ToTransferable<BioAssaySetInfo>

A bioassayset represents the current intensities of the raw data after some Transformation has been applied to it. The first transformation is called a root transformation. A bioassayset created by a root transformation is called a root bioassayset.

A bioassayset is created by the Transformation.newProduct(String, String, boolean) method. Bioassaysets can only be created if the transformation hasn't been committed to the database.

Version:

2.0

Author:

Nicklas

See Also:

Transformation.newProduct(String, String, boolean)

Last modified

$Date: 2010-04-20 10:02:16 +0200 (Tue, 20 Apr 2010) $

Field Summary

private Map<Integer,Integer>	bioAssaySpots Stores the result of getSpotCount(int).
private FilterBatcher	filterBatcher The one and only filter batcher for this bioassayset.
private org.hibernate.Query	findChildren Query to retrieve children for a bioassayset.
private Map<ExtraValueType,PositionExtraValueBatcher>	positionExtraValueBatchers Cache of already created position extra value batchers.
private SpotBatcher	spotBatcher The one and only spot batcher for this bioassayset.
private Map<ExtraValueType,SpotExtraValueBatcher>	spotExtraValueBatchers Cache of already created spot extra value batchers.
static 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

BioAssaySet(BioAssaySetData data)
Creates a new experiment item from the given data.

Method Summary

private void	addChildBioAssaySets(BioAssaySetData parent, Set<BioAssaySetData> all) Find all bioassaysets that are children to the specified parent (ie.
private void	checkAndCreateTables()
private void	countBioAssaySpots()
private void	countSpotsAndReporters() Count the number of unique reporters and spots in all bioassays in this bioassayset.
private void	deleteAnalysedData() Called when a bioassayset is about to be deleted.
Set<Annotatable>	getAnnotatableParents() Get the parent bioassay set (if any).
AnnotationSet	getAnnotationSet() Get the annotation set containing the annotations for this item.
ItemQuery<BioAssay>	getBioAssays() Get a query returning the bioassays that are part of this bioassayset.
static BioAssaySet	getById(DbControl dc, int id) Get a BioAssaySet item when you know the id.
(package private) DataCube	getDataCube() Get the data cube this biossayset stores it's data in.
(package private) DataCubeFilter	getDataCubeFilter() Get the data cube filter this biossayset uses to filter spot data.
short	getDataCubeFilterNo() Get the number of the filter that this bioassayset is using, or 0 if no filter is used.
(package private) DataCubeLayer	getDataCubeLayer() Get the data cube layer this biossayset stores it's data in.
short	getDataCubeLayerNo() Get the layer coordinate in the data cube that this bioassayset stores it's data in.
short	getDataCubeNo() Get the number of the data cube this bioassayset stores it's data in.
String	getDescription() Get the description for the item.
Experiment	getExperiment() Get the experiment this bioassayset belongs to.
ExtraValue	getExtraValue(ExtraValueType extraValueType) Get the extra value of the specified type in this bioassayset.
ItemQuery<ExtraValue>	getExtraValues() Get a query returning the extra values that are part of this bioassayset.
ItemQuery<ExtraValueType>	getExtraValueTypes() Get a query returning all extra values types that are used in this bioassay set.
FileSet	getFileSet() Get the file set that collects all files that holds data for this item.
FilterBatcher	getFilterBatcher() Get a batcher used to insert the position/column coordinates that remain after some filter has been applied to the spot data of a bioassayset.
IntensityTransform	getIntensityTransform() Get information about in what way the spot intensities has been transformed before they were stored in the database.
MappingBatcher	getMappingBatcher() Get a batcher used to insert mappings to raw data.
int	getMaxRawMappingsForSpot() Get the number of mappings to raw data spots for the spot with the most number of mappings.
String	getName() Get the name of the item.
(package private) static BioAssaySet	getNew(DbControl dc, Transformation transformation, DataCubeLayer layer) Create a new BioAssaySet item.
int	getNumFileReporters() Get the number of unique reporters for data that is stored in files.
int	getNumFileSpots() Get the number of spots that are stored in files.
int	getNumReporters() Get the number of unique reporters among all bioassays in this bioassayset.
int	getNumSpots() Get the number of spots in all bioassays in this bioassayset.
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 bioassay sets.
Platform	getPlatform() Get the platform the item is related to.
PositionBatcher	getPositionBatcher() Get a batcher that links position coordinates to reporters for the data cube this bioassayset uses.
DynamicPositionQuery	getPositionData() Get a query that returns position data for the data cube where this bioassayset is located.
<I> PositionExtraValueBatcher<I>	getPositionExtraValueBatcher(Class<I> clazz, ExtraValueType extraValueType, Job job) Get a batcher that is used to insert extra values per position of the specified type.
Protocol	getProtocol() Default implementation returns null.
static ItemQuery<BioAssaySet>	getQuery(Experiment experiment) Get a query configured to retrieve bioassaysets for a given experiment.
static ItemQuery<BioAssaySet>	getQuery(Transformation transformation) Get a query configured to retrieve bioassaysets created by a given transformation.
RawDataType	getRawDataType() Get the raw data type this experiment uses for the raw data.
(package private) SharedData	getSharedParent() Get the experiment.
SpotBatcher	getSpotBatcher() Get a batcher used to insert spot data for this bioassayset.
(package private) int	getSpotCount(int column) Get the number of spots in a single bioassay.
DynamicSpotQuery	getSpotData() Get a query that returns spot data for this bioassayset.
<I> SpotExtraValueBatcher<I>	getSpotExtraValueBatcher(Class<I> clazz, ExtraValueType extraValueType, Job job) Get a batcher that is used to insert extra values per spot of the specified type.
Transformation	getTransformation() Get the transformation that created this bioassayset.
ItemQuery<Transformation>	getTransformations() Get a query that return all transformations using this bioassayset as a source.
Item	getType() Get the type of item represented by the object.
PlatformVariant	getVariant() Get the platform variant the item is related to.
(package private) VirtualDb	getVirtualDb() Get the virtual database this bioassayset stores it's data in.
boolean	hasFileSet() Check if this item has a file set.
boolean	isAnnotated() Check if this item has an annotation set.
boolean	isRemoved() Check if the removed flag is set for this item.
BioAssay	newBioAssay(BioAssay parent) Create a new BioAssay in this bioassayset using a single parent.
BioAssay	newBioAssay(Collection<BioAssay> parents) Create a new BioAssay with links to multiple parent bioassays.
private BioAssay	newBioAssay(DataCubeColumn column, Collection<BioAssay> parents) Create a new bioassay and link to the parents.
BioAssay	newRootBioAssay(Collection<RawBioAssay> rawParents) Create a new BioAssay with links to raw bioassays.
Transformation	newTransformation(Job job) Create a new transformation using this bioassayset as it's source bioassayset.
(package private) void	onBeforeCommit(Transactional.Action action) On creation, count the number of spots and reporters in the bioassays attached to this bioassayset.
void	removeAnnotations() Remove all annotations from this item, by deleting the annotation set.
private void	setDataCubeFilter(DataCubeFilter filter)
private void	setDataCubeLayer(DataCubeLayer layer)
void	setDescription(String description) Set the description for the item.
private void	setExperiment(Experiment experiment) Set the experiment.
void	setIntensityTransform(IntensityTransform transform) Sets the transform used on the spot intensities before they were stored in the database.
void	setName(String name) Set the name of the item.
void	setNumFileReporters(int numReporters) Set the number of unique reporters for data that is stored in files.
void	setNumFileSpots(int numSpots) Set the number of spots that are stored in files.
void	setRemoved(boolean removed) Set the removed flag for this item.
private void	setTransformation(Transformation transformation) Set the transformation that created this bioassayset.
BioAssaySetInfo	toTransferable(BioAssaySetInfo info) Transfer the internal state to a transferable object.

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

getPluginPermissions, initPermissions

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOASSAYSET, getType()

spotBatcher

private SpotBatcher spotBatcher

The one and only spot batcher for this bioassayset.

See Also:

getSpotBatcher()

filterBatcher

private FilterBatcher filterBatcher

The one and only filter batcher for this bioassayset.

See Also:

getFilterBatcher()

spotExtraValueBatchers

private Map<ExtraValueType,SpotExtraValueBatcher> spotExtraValueBatchers

Cache of already created spot extra value batchers.

See Also:

getSpotExtraValueBatcher(Class, ExtraValueType, Job)

positionExtraValueBatchers

private Map<ExtraValueType,PositionExtraValueBatcher> positionExtraValueBatchers

Cache of already created position extra value batchers.

See Also:

getPositionExtraValueBatcher(Class, ExtraValueType, Job)

bioAssaySpots

private Map<Integer,Integer> bioAssaySpots

Stores the result of getSpotCount(int).

findChildren

private org.hibernate.Query findChildren

Query to retrieve children for a bioassayset.

See Also:

addChildBioAssaySets(BioAssaySetData, Set)

Constructor Detail

BioAssaySet

BioAssaySet(BioAssaySetData data)

Creates a new experiment item from the given data.

Parameters:

data - the data

Method Detail

getNew

static BioAssaySet getNew(DbControl dc,
                          Transformation transformation,
                          DataCubeLayer layer)
                   throws PermissionDeniedException,
                          InvalidDataException,
                          BaseException

Create a new BioAssaySet item.

Parameters:

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

transformation - The transformation that created the bioassayset

layer - The data cube layer where the bioassayset should store it's data

Returns:

The new BioAssaySet item

Throws:

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

InvalidDataException - If the transformation is null

BaseException - If there is an error

See Also:

Transformation.newProduct(String, String, boolean)

getById

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

Get a BioAssaySet 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 BioAssaySet 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<BioAssaySet> getQuery(Experiment experiment)
                                       throws InvalidDataException

Get a query configured to retrieve bioassaysets for a given experiment.

Parameters:

experiment - The experiment to retreive bioassaysets for, null is not allowed

Returns:

An ItemQuery object

Throws:

InvalidDataException - If the parameter is null.

getQuery

public static ItemQuery<BioAssaySet> getQuery(Transformation transformation)
                                       throws InvalidDataException

Get a query configured to retrieve bioassaysets created by a given transformation.

Parameters:

transformation - The transformation to retreive bioassaysets for, null is not allowed

Returns:

An ItemQuery object

Throws:

InvalidDataException - If the transformation parameter is null.

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

isRemoved

public boolean isRemoved()

Description copied from interface: Removable

Check if the removed flag is set for this item.

Specified by:

isRemoved in interface Removable

Returns:

TRUE if the item is flagged as removed, FALSE otherwise

setRemoved

public void setRemoved(boolean removed)
                throws PermissionDeniedException

Description copied from interface: Removable

Set the removed flag for this item.

Specified by:

setRemoved in interface Removable

Parameters:

removed - TRUE if the item should be flagged as removed, FALSE otherwise

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.DELETE permission for setting the flag to TRUE or Permission.WRITE permission for setting the flag to FALSE

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 (if any).

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

Since:

2.2

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

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
              throws BaseException

On creation, count the number of spots and reporters in the bioassays attached to this bioassayset. On deletion, delete all analysed data in this bioassayset and all child bioassaysets.

Overrides:

onBeforeCommit in class BasicItem<BioAssaySetData>

Throws:

BaseException - If there is an error

See Also:

Transactional, Core API overview - Transaction handling, Coding rules and guidelines for item classes

getSharedParent

SharedData getSharedParent()

Get the experiment.

Specified by:

getSharedParent in class ChildItem<BioAssaySetData>

Returns:

The parent item

getPermissionForWriteDeleteAndCreate

Permission getPermissionForWriteDeleteAndCreate()

USE permission is enough to be able to manage bioassay sets.

Overrides:

getPermissionForWriteDeleteAndCreate in class ChildItem<BioAssaySetData>

toTransferable

public BioAssaySetInfo toTransferable(BioAssaySetInfo info)

Description copied from interface: ToTransferable

Transfer the internal state to a transferable object. The method should return the same object that is passed in as an argument.

Specified by:

toTransferable in interface ToTransferable<BioAssaySetInfo>

Parameters:

info - The transferable object to use

Returns:

The transferable object with values set.

Since:

2.5

getExperiment

public Experiment getExperiment()
                         throws PermissionDeniedException,
                                BaseException

Get the experiment this bioassayset 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

setExperiment

private void setExperiment(Experiment experiment)
                    throws PermissionDeniedException,
                           InvalidDataException

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

Throws:

PermissionDeniedException

InvalidDataException

getTransformation

public Transformation getTransformation()
                                 throws PermissionDeniedException,
                                        BaseException

Get the transformation that created this bioassayset.

Returns:

A Transformation object

Throws:

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

BaseException - If there is another error

setTransformation

private void setTransformation(Transformation transformation)
                        throws PermissionDeniedException,
                               InvalidDataException

Set the transformation that created this bioassayset. This cannot be changed after the bioassayset has been created.

Throws:

PermissionDeniedException

InvalidDataException

getRawDataType

public RawDataType getRawDataType()

Get the raw data type this experiment uses for the raw data. The raw data type cannot be changed once the experiment has been created.

Returns:

A RawDataType object

getNumReporters

public int getNumReporters()

Get the number of unique reporters among all bioassays in this bioassayset.

getNumSpots

public int getNumSpots()

Get the number of spots in all bioassays in this bioassayset.

getNumFileReporters

public int getNumFileReporters()

Get the number of unique reporters for data that is stored in files.

Since:

2.8

setNumFileReporters

public void setNumFileReporters(int numReporters)

Set the number of unique reporters for data that is stored in files.

Parameters:

numReporters - The number of reporters

Since:

2.8

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

getMaxRawMappingsForSpot

public int getMaxRawMappingsForSpot()

Get the number of mappings to raw data spots for the spot with the most number of mappings. For most bioassay sets this value is probably 1. After a merge, the count can be higher which may require some plugins to behave differently when using values from the raw data table.

Since:

2.2

getIntensityTransform

public IntensityTransform getIntensityTransform()

Get information about in what way the spot intensities has been transformed before they were stored in the database.

Since:

2.12

setIntensityTransform

public void setIntensityTransform(IntensityTransform transform)

Sets the transform used on the spot intensities before they were stored in the database. NOTE! Calling this method doesn't change the data in the database!

Parameters:

transform - The transform that was used to store the data

Since:

2.12

getDataCubeNo

public short getDataCubeNo()

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

See Also:

getDataCubeLayerNo(), getDataCubeFilterNo()

getDataCubeLayerNo

public short getDataCubeLayerNo()

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

See Also:

getDataCubeNo(), getDataCubeFilterNo()

getDataCubeFilterNo

public short getDataCubeFilterNo()

Get the number of the filter that this bioassayset is using, or 0 if no filter is used.

Returns:

The number of the filter or 0 if no filter is used

See Also:

getDataCubeLayerNo(), getDataCubeNo()

getVirtualDb

VirtualDb getVirtualDb()

Get the virtual database this bioassayset stores it's data in.

getDataCube

DataCube getDataCube()
               throws PermissionDeniedException,
                      BaseException

Get the data cube this biossayset stores it's data in.

Throws:

PermissionDeniedException

BaseException

getDataCubeLayer

DataCubeLayer getDataCubeLayer()

Get the data cube layer this biossayset stores it's data in.

setDataCubeLayer

private void setDataCubeLayer(DataCubeLayer layer)

getDataCubeFilter

DataCubeFilter getDataCubeFilter()

Get the data cube filter this biossayset uses to filter spot data.

setDataCubeFilter

private void setDataCubeFilter(DataCubeFilter filter)

newTransformation

public Transformation newTransformation(Job job)
                                 throws PermissionDeniedException,
                                        BaseException

Create a new transformation using this bioassayset as it's source bioassayset.

Parameters:

job - The job that executed the transformation

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the experiment this bioassayset belongs to

BaseException - If there is another error

getTransformations

public ItemQuery<Transformation> getTransformations()

Get a query that return all transformations using this bioassayset as a source.

Returns:

An ItemQuery object

See Also:

Transformation.getQuery(BioAssaySet)

newRootBioAssay

public BioAssay newRootBioAssay(Collection<RawBioAssay> rawParents)
                         throws PermissionDeniedException,
                                InvalidDataException,
                                BaseException

Create a new BioAssay with links to raw bioassays. This type of bioassay can only be created if the transformation that created it is a root transformation. New bioassays can only be created if the bioassayset hasn't been committed to the database.

The raw bioassay collection should contain only those raw bioassays whose spots have been used to calculate the intensities stored in this bioassay.

Parameters:

rawParents - A collection containing the raw bioassays that are the parents of this bioassay

Returns:

The new BioAssay item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the experiment of if the bioassayset has been committed to the database

InvalidDataException - If this bioassayset is not a product of a root transformation or if any of the raw bioassay parents isn't a member of the transformation

BaseException - If something else goes wrong.

See Also:

newBioAssay(BioAssay), newBioAssay(Collection)

newBioAssay

public BioAssay newBioAssay(BioAssay parent)
                     throws InvalidDataException,
                            PermissionDeniedException

Create a new BioAssay in this bioassayset using a single parent. The data cube column coordinate of the new bioassay is set to the same as that of the parent. The bioassayset of the parent bioassay must match the bioassayset set of the source of the transformation and this bioassayset must use the same data cube as the source bioassayset. The new bioassay is automatically linked to the same raw bioassays as the parent bioassay.

New bioassays can only be created if the bioassayset hasn't been committed to the database.

Parameters:

parent - The parent bioassay

Returns:

The new bioassay

Throws:

InvalidDataException - If the parent is null or it's bioassayset is not the same as the source bioassayset of the transformation or if the data cube of the source is not the same as the data cube for this bioassayset

PermissionDeniedException - If the bioassayset has already been committed to the database

See Also:

newBioAssay(Collection), newRootBioAssay(Collection)

newBioAssay

public BioAssay newBioAssay(Collection<BioAssay> parents)

Create a new BioAssay with links to multiple parent bioassays. This type of bioassay can only be created if the transformation that created it isn't a root transformation, since a root transformation can't have a parent bioassayset. This type of bioassay must be created if this bioassayset uses a different data cube than the bioassayset that is the source of the transformation. The new bioassay is automatically linked to the same raw bioassays as the parent bioassay.

New bioassays can only be created if the bioassayset hasn't been committed to the database.

Parameters:

parents - A collection containing the bioassays that are the parents of this bioassay

Returns:

The new BioAssay item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the experiment of if the bioassayset has been committed to the database

InvalidDataException - If this bioassayset is the product of a root transformation or if any of the bioassay parents isn't a member source bioassayset of the transformation

See Also:

newBioAssay(BioAssay), newRootBioAssay(Collection)

newBioAssay

private BioAssay newBioAssay(DataCubeColumn column,
                             Collection<BioAssay> parents)

Create a new bioassay and link to the parents. Assume that all neccessary checks has been made by calling code. If the collections contains only a single parent, the name will be copied to the child.

getBioAssays

public ItemQuery<BioAssay> getBioAssays()

Get a query returning the bioassays that are part of this bioassayset.

Returns:

An ItemQuery object

getExtraValues

public ItemQuery<ExtraValue> getExtraValues()

Get a query returning the extra values that are part of this bioassayset. To add extra values use one of the methods that returns a batcher.

Returns:

An ItemQuery object

See Also:

getSpotExtraValueBatcher(Class, ExtraValueType, Job), getPositionExtraValueBatcher(Class, ExtraValueType, Job)

getExtraValueTypes

public ItemQuery<ExtraValueType> getExtraValueTypes()

Get a query returning all extra values types that are used in this bioassay set.

Returns:

An ItemQuery object

Since:

2.15

See Also:

getExtraValues(), getExtraValue(ExtraValueType)

getExtraValue

public ExtraValue getExtraValue(ExtraValueType extraValueType)
                         throws BaseException

Get the extra value of the specified type in this bioassayset. To add extra values use one of the methods that returns a batcher.

Parameters:

extraValueType - For which extra value should be returned.

Returns:

An ExtraValue item, or null if no extra value of the specified type has been created for this bioassayset

Throws:

BaseException - If something fails when getting the extra value.

See Also:

getSpotExtraValueBatcher(Class, ExtraValueType, Job), getPositionExtraValueBatcher(Class, ExtraValueType, Job)

getPositionBatcher

public PositionBatcher getPositionBatcher()
                                   throws PermissionDeniedException

Get a batcher that links position coordinates to reporters for the data cube this bioassayset uses. The links must be created before the data cube is committed to the database. This means that only the first bioassayset in a data cube can create the links to reporters. To insert extra values (which can be done at any time) based on the position use the getPositionExtraValueBatcher(Class, ExtraValueType, Job) method to get a batcher for that.

Returns:

A PositionBatcher object

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or if the data cube has already been committed to the database

See Also:

getPositionExtraValueBatcher(Class, ExtraValueType, Job)

getMappingBatcher

public MappingBatcher getMappingBatcher()
                                 throws PermissionDeniedException

Get a batcher used to insert mappings to raw data. The links must be created before the data cube is committed to the database. This means that only the first bioassayset in a data cube can create the links to raw data.

Returns:

A MappingBatcher object

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or if the data cube has already been committed to the database

getSpotBatcher

public SpotBatcher getSpotBatcher()
                           throws PermissionDeniedException

Get a batcher used to insert spot data for this bioassayset. If this bioassayset uses the same layer as another bioassayset or if this bioassayset has already been committed to the database no more intensities can be inserted. To insert extra values (which can be done at any time) based on the position use the getSpotExtraValueBatcher(Class, ExtraValueType, Job) method to get a batcher for that.

Returns:

A SpotBatcher object

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or if the data cube layer has already been committed to the database

See Also:

getSpotExtraValueBatcher(Class, ExtraValueType, Job)

getFilterBatcher

public FilterBatcher getFilterBatcher()
                               throws PermissionDeniedException

Get a batcher used to insert the position/column coordinates that remain after some filter has been applied to the spot data of a bioassayset. Filter information cannot be inserted after the bioassayset has been committed to the database. Calling this method and not inserting any position/column coordinates will result in a bioassayset with no data.

Returns:

A FilterBatcher object

Throws:

PermissionDeniedException - If the bioassayset has already been committed to the database or if the logged in user doesn't have write permission

See Also:

getSpotBatcher()

getSpotExtraValueBatcher

public <I> SpotExtraValueBatcher<I> getSpotExtraValueBatcher(Class<I> clazz,
                                                             ExtraValueType extraValueType,
                                                             Job job)
                                                  throws PermissionDeniedException,
                                                         InvalidDataException

Get a batcher that is used to insert extra values per spot of the specified type. A bioassay set can only have one set of extra values for each type. If this method is called more than once in the same transaction with the same extra value type parameter, the same batcher is returned.

Parameters:

clazz - The class object for the values, ie. Integer.class, Float.class or String.class

extraValueType - The definition of the extra value type

job - The job that is doing the extra value calculations or null

Returns:

A SpotExtraValueBatcher object

Throws:

PermissionDeniedException - If the loggged in user doesn't have write permission for the bioassay set

InvalidDataException - If the extra value type is null or has a value type that doesn't match the specified class

See Also:

getSpotBatcher()

getPositionExtraValueBatcher

public <I> PositionExtraValueBatcher<I> getPositionExtraValueBatcher(Class<I> clazz,
                                                                     ExtraValueType extraValueType,
                                                                     Job job)
                                                          throws PermissionDeniedException,
                                                                 InvalidDataException

Get a batcher that is used to insert extra values per position of the specified type. A bioassay set can only have one set of extra values for each type. If this method is called more than once in the same transaction with the same extra value type parameter, the same batcher is returned.

Parameters:

clazz - The class object for the values, ie. Integer.class, Float.class or String.class

extraValueType - The definition of the extra value type

job - The job that is doing the extra value calculations or null

Returns:

A PositionExtraValueBatcher object

Throws:

PermissionDeniedException - If the loggged in user doesn't have write permission for the bioassay set

InvalidDataException - If the extra value type is null or has a value type that doesn't match the specified class

getSpotData

public DynamicSpotQuery getSpotData()

Get a query that returns spot data for this bioassayset. The query will select column, position and spot intensities by default. Ie.

// Default query -- filter is only joined if the bioassayset is filtered
SELECT spt.column, spt.position, spt.ch1, spt.ch2, ...
FROM Dynamic#PerSpot spt
[ JOIN Dynamic#Filter flt 
   ON flt.cube = spt.cube AND flt.column = spt.column 
   AND flt.position = spt.position ]
WHERE spt.cube = <cube_no> AND spt.layer = <layer_no> 
   [ AND flt.filter = <filter_no> ]

Note! If the bioassay set contains transformed intensities, the default selection will un-transform the values.

Returns:

A DynamicSpotQuery object

getPositionData

public DynamicPositionQuery getPositionData()

Get a query that returns position data for the data cube where this bioassayset is located. The query will only select the position by default. The returned result doesn't depend on what spots are located in this bioassayset. Ie. the query will return the same result for all bioassaysets in the same data cube. If you need position data that depends on the spots in the bioassayset, use the getSpotData() method and then join reporters using the DynamicSpotQuery.joinReporters(JoinType) method.

// Default query
SELECT pos.position
FROM Dynamic#PerPosition AS pos
WHERE pos.cube = <cube_no>

Returns:

A DynamicPositionQuery object

countSpotsAndReporters

private void countSpotsAndReporters()

Count the number of unique reporters and spots in all bioassays in this bioassayset. This method in called by the onBeforeCommit method to calculate the numbers (which cannot be changed later) before the bioassayset is committed to the database.

getSpotCount

int getSpotCount(int column)

Get the number of spots in a single bioassay. This method in called by the BioAssay.onBeforeCommit method to calculate the numbers (which cannot be changed later) before the bioassay is saved to the database. The reason it is located here is that a single query can calculate the spots for all bioassays in a one go.

countBioAssaySpots

private void countBioAssaySpots()

See Also:

getSpotCount(int)

checkAndCreateTables

private void checkAndCreateTables()

deleteAnalysedData

private void deleteAnalysedData()
                         throws BaseException

Called when a bioassayset is about to be deleted. Finds which data cubes, layers, filters and extra values that are exclusively used by this bioassayset or one of the child bioassaysets (which are deleted by Hibernate cascade). Then, it deletes all those items. A bug in this method may cause stale data to be left in the database (bad) or data used by other bioassaysets to be deleted (even worse). For each type of item it is a three-step process:

1. Find the items used by at least one of the bioassaysets that are going to be deleted
2. Among the items found, find out if any of them are also used by other bioassaysets that are not going to be deleted
3. Delete only those items that are left

Throws:

BaseException

addChildBioAssaySets

private void addChildBioAssaySets(BioAssaySetData parent,
                                  Set<BioAssaySetData> all)

Find all bioassaysets that are children to the specified parent (ie. the product of a transformation using the parent as a source) and add those the all set. The method is then called recursively to add the grandchildren and so on.