net.sf.basedb.core
Class RawBioAssay

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<D>
                  net.sf.basedb.core.AnnotatedItem<RawBioAssayData>
                      net.sf.basedb.core.RawBioAssay

All Implemented Interfaces:

AccessControlled, Annotatable, Controlled, DiskConsumable, FileStoreEnabled, Identifiable, Nameable, Ownable, Registered, Removable, Shareable, ToTransferable<RawBioAssayInfo>

public class RawBioAssay
extends AnnotatedItem<RawBioAssayData>
implements DiskConsumable, FileStoreEnabled, ToTransferable<RawBioAssayInfo>, Registered

A rawbioassay represents the raw data generated from a single Scan. A raw bioassay must have a RawDataType which specifies the data columns generated by the Software.

Raw data is added by a RawDataBatcher object. You can get a batcher for this raw bioassay by calling the getRawDataBatcher(FeatureIdentificationMethod, Job) method.

Version:

2.0

Author:

Nicklas

Last modified

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

Field Summary

private boolean	arrayDesignHasBeenSet
static int	MAX_HEADER_NAME_LENGTH The maximum length of the name of a header that can be stored in the database.
static int	MAX_HEADER_VALUE_LENGTH The maximum length of the value of a header that can be stored in the database.
private boolean	protocolHasBeenSet
private RawDataBatcher	rawDataBatcher
private boolean	softwareHasBeenSet
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

RawBioAssay(RawBioAssayData data)

Method Summary

void	deleteRawData() Delete the raw data that has been added to the database for this raw bioassay.
Set<Annotatable>	getAnnotatableParents() Get the scan, if any.
ArrayDesign	getArrayDesign() Get the ArrayDesign this raw data uses.
int	getArrayNum() Get the hybridization array number this raw bioassay is linked to.
static RawBioAssay	getById(DbControl dc, int id) Get a RawBioAssay object when you know the id.
long	getBytes() Get the absolute number of bytes this item uses.
long	getDifference() Always 0.
DynamicRawDataQuery	getDynamicRawData() Get a dynamic query that returns the raw data of this raw bioassay.
Date	getEntryDate() Get the date that the item was registered in the database.
ItemQuery<Experiment>	getExperiments() Get a query that returns all experiments where this raw bioassay is used.
FileSet	getFileSet() Get the file set that collects all files that holds data for this item.
String	getHeader(String name) Get the value for the raw data header with the specified name.
Set<String>	getHeaderNames() Get the names of all raw data headers.
Job	getJob() Get the job that imported data to this raw bioassay.
Location	getLocation() Always Location.PRIMARY.
static RawBioAssay	getNew(DbControl dc, Platform platform, RawDataType rawDataType) Create a new raw bioassay for a specific platform and/or raw data type.
static RawBioAssay	getNew(DbControl dc, PlatformVariant variant, RawDataType rawDataType) Create a new raw bioassay for a specific platform variant.
static RawBioAssay	getNew(DbControl dc, RawDataType rawDataType) Deprecated. Use getNew(DbControl, Platform, RawDataType) or getNew(DbControl, PlatformVariant, RawDataType) instead. This method will set the platform to Platform.GENERIC.
int	getNumDbSpots() Get the number of spots on this raw bioassay that are stored in the database.
int	getNumFileSpots() Get the number of spots on this raw bioassay that are stored inside files.
Collection<FileSet>	getParentFileSets() Get the file set from the array design, if it exists.
Platform	getPlatform() Get the platform the item is related to.
Protocol	getProtocol() Get the Protocol used while analysing the scanned images.
static ItemQuery<RawBioAssay>	getQuery() Get a query configured to retrieve raw bioassays.
String	getQuotaTypeSystemId() Always QuotaType.RAW_DATA.
DataQuery<RawData>	getRawData() Get a query that returns the raw data of this raw bioassay.
RawDataBatcher	getRawDataBatcher() Deprecated. Use getRawDataBatcher(FeatureIdentificationMethod, Job) instead
RawDataBatcher	getRawDataBatcher(FeatureIdentificationMethod fiMethod) Deprecated. Use getRawDataBatcher(FeatureIdentificationMethod, Job) instead.
RawDataBatcher	getRawDataBatcher(FeatureIdentificationMethod fiMethod, Job job) Get a raw data batcher object which can be used to add raw data to the raw bioassay.
RawData	getRawDataById(int id) Get a raw data spot when you know the id.
RawData	getRawDataById(int id, boolean forceInitialization) Get a raw data spot when you know the id.
RawDataType	getRawDataType() Get the raw data type this raw bioassay uses for the raw data.
DataQuery<ReporterData>	getReporters() Get a query that returns the reporters on this raw bioassay.
Scan	getScan() Get the Scan this raw bioassay is created from.
Software	getSoftware() Get the Software used while analysing the scanned images.
SpotImages	getSpotImages() Get the SpotImages item used to generate spot images for this raw bioassay.
int	getSpots() Deprecated. Use getNumDbSpots() or getNumFileSpots() instead. This method first checks the database and if not 0, it returns that value, otherwise it returns the number of file spots
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Experiment:s using this raw bioassay Transformation:s using this raw bioassay
PlatformVariant	getVariant() Get the platform variant the item is related to.
boolean	hasArrayDesign() Check if this raw bioassay is connected to an array design or not.
boolean	hasData() If raw data has been added to this raw bioassay or not.
boolean	hasFileSet() Check if this item has a file set.
boolean	hasSpotImages() Check if spot images exists for this raw bioassay or not.
boolean	isFileOnlyPlatform() Check if this raw bioassay uses a file-only platform or variant.
boolean	isPlatform(String externalId) Check if the platform/variant of this raw bioassay has the given external ID.
boolean	isUsed() Check if: An Experiment is using this raw bioassay A Transformation is using this raw bio raw data type will also be updated.
(package private) void	onBeforeCommit(Transactional.Action action) Delete raw data if it exists.
void	removeHeader(String name) Remove a specific header from the raw bioassay.
void	removeHeaders() Remove all headers from the raw bioassay.
void	setArrayDesign(ArrayDesign arrayDesign) Set the ArrayDesign this raw data uses.
void	setArrayNum(int arrayNum) Set the hybridization array number this raw bioassay is linked to.
void	setHeader(String name, String value) Set the value for a raw data header.
void	setNumFileSpots(int numSpots) Set the number of spots that are stored in files.
void	setPlatform(Platform platform, RawDataType rawDataType) Set the platform and raw data type of the raw bioassay.
(package private) void	setProjectDefaults(Project activeProject) Set software, protocol and array design from project default settings.
void	setProtocol(Protocol protocol) Set the Protocol used while analysing the scanned images.
void	setRawDataType(RawDataType rawDataType) Deprecated. Use setPlatform(Platform, RawDataType) or setVariant(PlatformVariant, RawDataType) instead
void	setScan(Scan scan) Set the Scan this raw bioassay is created from.
void	setSoftware(Software software) Set the Software used while analysing the scanned images.
void	setVariant(PlatformVariant variant, RawDataType rawDataType) Set the platform and variant of the raw bioassay.
RawBioAssayInfo	toTransferable(RawBioAssayInfo info) Transfer the internal state to a transferable object.
void	updateArrayDesign(ArrayDesign arrayDesign, FeatureIdentificationMethod fiMethod, ProgressReporter progress) Set the ArrayDesign this raw data uses.
void	updateArrayDesign(ArrayDesign arrayDesign, ProgressReporter progress) Deprecated. Use updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter) instead
boolean	useDifference() Always FALSE.
private void	validateFeatures(DbControl dc, ArrayDesign design, FeatureIdentificationMethod fiMethod, boolean update, ProgressReporter progress) Validate that the features/reporters of the raw data matches the features/reporter on the array design.

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

getAnnotationSet, isAnnotated, removeAnnotations, toTransferable

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

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

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

getItemKey, getProjectKey, initPermissions, isShared, setItemKey, setProjectKey, toTransferable

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

getOwner, isOwner, setOwner, takeOwnership, toTransferable

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, 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.Ownable

getOwner, isOwner, setOwner, takeOwnership

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.RAWBIOASSAY, getType()

MAX_HEADER_NAME_LENGTH

public static final int MAX_HEADER_NAME_LENGTH

The maximum length of the name of a header that can be stored in the database. Check the name length against this value before calling setHeader(String, String) to avoid exceptions.

See Also:

Constant Field Values

MAX_HEADER_VALUE_LENGTH

public static final int MAX_HEADER_VALUE_LENGTH

The maximum length of the value of a header that can be stored in the database. Check the value length against this value before calling setHeader(String, String) to avoid exceptions.

See Also:

Constant Field Values

rawDataBatcher

private RawDataBatcher rawDataBatcher

softwareHasBeenSet

private boolean softwareHasBeenSet

protocolHasBeenSet

private boolean protocolHasBeenSet

arrayDesignHasBeenSet

private boolean arrayDesignHasBeenSet

Constructor Detail

RawBioAssay

RawBioAssay(RawBioAssayData data)

Method Detail

getNew

public static RawBioAssay getNew(DbControl dc,
                                 RawDataType rawDataType)
                          throws BaseException

Deprecated. Use getNew(DbControl, Platform, RawDataType) or getNew(DbControl, PlatformVariant, RawDataType) instead. This method will set the platform to Platform.GENERIC.

Create a new RawBioAssay item. The platform/variant will automatically be set to the values returned by RawDataType.getPlatform(DbControl) and RawDataType.getVariant(DbControl). If both return null the Platform.GENERIC is used.

Parameters:

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

rawDataType - The data type of the raw data

Returns:

The new RawBioAssay item

Throws:

BaseException - If there is an error

getNew

public static RawBioAssay getNew(DbControl dc,
                                 Platform platform,
                                 RawDataType rawDataType)

Create a new raw bioassay for a specific platform and/or raw data type. If the platform is locked to a specific raw data type, the rawDataType parameter is ignored. If the platform isn't locked the raw data type is required and must be a database-based raw data type. Ie. RawDataType.isStoredInDb() must return true.

Parameters:

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

platform - The platform of the new raw bioassay, null is not allowed

rawDataType - The raw data type of the raw bioassay (required if the platform isn't locked to a specific raw data type)

Returns:

The new RawBioAssay item

Since:

2.5

getNew

public static RawBioAssay getNew(DbControl dc,
                                 PlatformVariant variant,
                                 RawDataType rawDataType)

Create a new raw bioassay for a specific platform variant. If the variant is locked to a specific raw data type, the rawDataType parameter is ignored. If the variant isn't locked the raw data type is required and must be a database-based raw data type. Ie. RawDataType.isStoredInDb() must return true.

Parameters:

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

variant - The platform variant of the new raw bioassay, null is not allowed

rawDataType - The raw data type of the raw bioassay (required if the platform isn't locked to a specific raw data type)

Returns:

The new RawBioAssay item

Since:

2.5

getById

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

Get a RawBioAssay 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 RawBioAssay 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 item

BaseException - If there is another error

getQuery

public static ItemQuery<RawBioAssay> getQuery()

Get a query configured to retrieve raw bioassays.

Returns:

An ItemQuery object

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

useDifference

public boolean useDifference()

Always FALSE.

Specified by:

useDifference in interface DiskConsumable

Returns:

TRUE if the item reports the difference, FALSE if it reports the absolute

See Also:

DiskConsumable.getBytes(), DiskConsumable.getDifference()

getBytes

public long getBytes()

Description copied from interface: DiskConsumable

Get the absolute number of bytes this item uses. All items must report this number.

Specified by:

getBytes in interface DiskConsumable

Returns:

The absolute number of bytes the item uses

See Also:

DiskConsumable.useDifference(), DiskConsumable.getDifference()

getDifference

public long getDifference()

Always 0.

Specified by:

getDifference in interface DiskConsumable

Returns:

The difference in bytes between now and when the item was loaded, or 0 if this item doesn't report differences

getQuotaTypeSystemId

public String getQuotaTypeSystemId()

Always QuotaType.RAW_DATA.

Specified by:

getQuotaTypeSystemId in interface DiskConsumable

Returns:

The systemid of the QuotaType

getLocation

public Location getLocation()

Always Location.PRIMARY.

Specified by:

getLocation in interface DiskConsumable

Returns:

The location

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the scan, if any.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

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:

2.5

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:

2.5

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:

A platform or null if the items is not related to any platform.

Since:

2.5

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:

A platform or null if the items is not related to any variant.

Since:

2.5

getParentFileSets

public Collection<FileSet> getParentFileSets()

Get the file set from the array design, if it exists.

Specified by:

getParentFileSets in interface FileStoreEnabled

Returns:

A collection of FileSet or null

Since:

2.5

getEntryDate

public Date getEntryDate()

Description copied from interface: Registered

Get the date that the item was registered in the database.

Specified by:

getEntryDate in interface Registered

Returns:

A date or null if this is not known

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• An Experiment is using this raw bioassay
• A Transformation is using this raw bio raw data type will also be updated. The platform can't be changed if raw data has been imported to the database.assay

Overrides:

isUsed in class BasicItem<RawBioAssayData>

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()

Get all:

• Experiment:s using this raw bioassay
• Transformation:s using this raw bioassay

  Overrides:

  getUsingItems in class BasicItem<RawBioAssayData>

  Returns:

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

  Since:

  2.2

  See Also:

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

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
              throws BaseException

Delete raw data if it exists.

Overrides:

onBeforeCommit in class SharedItem<RawBioAssayData>

Throws:

BaseException - If there is another error

See Also:

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

setProjectDefaults

void setProjectDefaults(Project activeProject)
                  throws BaseException

Set software, protocol and array design from project default settings.

Overrides:

setProjectDefaults in class BasicItem<RawBioAssayData>

Parameters:

activeProject - The currently active project

Throws:

BaseException

Since:

2.9

toTransferable

public RawBioAssayInfo toTransferable(RawBioAssayInfo 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<RawBioAssayInfo>

Parameters:

info - The transferable object to use

Returns:

The transferable object with values set.

Since:

2.5

setPlatform

public void setPlatform(Platform platform,
                        RawDataType rawDataType)

Set the platform and raw data type of the raw bioassay. This method will set the variant to null. Use setVariant(PlatformVariant, RawDataType) if you want to set a specific variant. If the platform is locked to a raw data type, the rawDataType parameter is ignored. If the platform isn't locked the raw data type must be a database-based raw data type. Ie. RawDataType.isStoredInDb() must return true.

Parameters:

platform - The new platform, null is not allowes

rawDataType - The raw data type, required if the platform doesn't specify a raw data type

Throws:

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

InvalidDataException - If platform is null or if the raw data type is not properly specified

Since:

2.5

setVariant

public void setVariant(PlatformVariant variant,
                       RawDataType rawDataType)

Set the platform and variant of the raw bioassay. This method will automatically set the platform to PlatformVariant.getPlatform(). If the platform variant is locked to a raw data type, the raw data type is also updated. The platform variant can't be changed if raw data has been imported to the database.

Parameters:

variant - The new platform variant

rawDataType - The rawdata type for this platform variant. Null is allowed if rawDataType already has been set.

Throws:

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

InvalidDataException - If variant is null

Since:

2.5

isPlatform

public boolean isPlatform(String externalId)

Check if the platform/variant of this raw bioassay has the given external ID.

Parameters:

externalId - The external ID to match

Returns:

TRUE if either the variant of platform matches the external ID

Since:

2.5

isFileOnlyPlatform

public boolean isFileOnlyPlatform()

Check if this raw bioassay uses a file-only platform or variant. If the raw bioassay has a platform variant, the setting from the variant is returned, otherwise the setting from the platform.

Returns:

TRUE if this raw bioassay use a file-only variant / platform

Since:

2.5

getRawDataType

public RawDataType getRawDataType()

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

Returns:

A RawDataType object

setRawDataType

public void setRawDataType(RawDataType rawDataType)
                    throws PermissionDeniedException,
                           InvalidDataException

Deprecated. Use setPlatform(Platform, RawDataType) or setVariant(PlatformVariant, RawDataType) instead

Set the raw data type. The raw data type cannot be changed if raw data has been added to the database.

Parameters:

rawDataType - The raw data type, null is not allowed

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay or spots has already been added

InvalidDataException

getJob

public Job getJob()
           throws PermissionDeniedException,
                  BaseException

Get the job that imported data to this raw bioassay.

Returns:

A Job object, ot null if this information is not available

Throws:

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

BaseException - If there is another error

Since:

2.7

getArrayNum

public int getArrayNum()

Get the hybridization array number this raw bioassay is linked to. The default value is 1.

Since:

2.6

setArrayNum

public void setArrayNum(int arrayNum)

Set the hybridization array number this raw bioassay is linked to. The value should be between 1 and the number of arrays specified by the hybridization, Hybridization.getNumArrays().

Parameters:

arrayNum - A value > 0

Throws:

NumberOutOfRangeException - If the value is <=0

Since:

2.6

getScan

public Scan getScan()
             throws PermissionDeniedException,
                    BaseException

Get the Scan this raw bioassay is created from.

Returns:

The Scan item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the scanner

BaseException - If there is another error.

setScan

public void setScan(Scan scan)
             throws PermissionDeniedException

Set the Scan this raw bioassay is created from.

Parameters:

scan - The scan or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay use permission for the scan

BaseException - If there is another error

getSoftware

public Software getSoftware()
                     throws PermissionDeniedException,
                            BaseException

Get the Software used while analysing the scanned images.

Returns:

The Software item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the software

BaseException - If there is another error.

setSoftware

public void setSoftware(Software software)
                 throws PermissionDeniedException

Set the Software used while analysing the scanned images.

Parameters:

software - The software or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay use permission for the scanner

BaseException - If there is another error

getProtocol

public Protocol getProtocol()
                     throws PermissionDeniedException,
                            BaseException

Get the Protocol used while analysing the scanned images.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem<RawBioAssayData>

Returns:

The Protocol item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the protocol

BaseException - If there is another error.

setProtocol

public void setProtocol(Protocol protocol)
                 throws PermissionDeniedException

Set the Protocol used while analysing the scanned images.

Parameters:

protocol - The protocol or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay use permission for the protocol

BaseException - If there is another error

getArrayDesign

public ArrayDesign getArrayDesign()
                           throws PermissionDeniedException,
                                  BaseException

Get the ArrayDesign this raw data uses. This should normally be the same as the array design reached via the hybridization, but doesn't have to be.

Returns:

The ArrayDesign item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the array design

BaseException - If there is another error.

setArrayDesign

public void setArrayDesign(ArrayDesign arrayDesign)
                    throws PermissionDeniedException

Set the ArrayDesign this raw data uses. The array design can't be changed with this method once raw data spots has been added. Use the updateArrayDesign(ArrayDesign, ProgressReporter) to do that.

Parameters:

arrayDesign - The ArrayDesign item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay use permission for the array design or spots has already been added

BaseException - If there is another error

updateArrayDesign

public void updateArrayDesign(ArrayDesign arrayDesign,
                              ProgressReporter progress)
                       throws PermissionDeniedException,
                              InvalidDataException

Deprecated. Use updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter) instead

Throws:

PermissionDeniedException

InvalidDataException

updateArrayDesign

public void updateArrayDesign(ArrayDesign arrayDesign,
                              FeatureIdentificationMethod fiMethod,
                              ProgressReporter progress)
                       throws PermissionDeniedException,
                              InvalidDataException

Set the ArrayDesign this raw data uses. If data has already been imported to the raw bioassay, the reporters for each position on the new array design must match the positions of reporters already present in the raw bioassay.

Parameters:

arrayDesign - The ArrayDesign item or null if not known

fiMethod - The method to use for identifying features on the new array design. Use null to use the method choosen by the new array design. The FeatureIdentificationMethod.FEATURE_ID will not work unless the raw bioassay is already connected to an array design which has features with external ID:s

progress - An optional progress reporter

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the raw bioassay use permission for the array design

InvalidDataException - If the features of the new array design doesn't match the raw data

BaseException - If there is another error

Since:

2.6

hasArrayDesign

public boolean hasArrayDesign()

Check if this raw bioassay is connected to an array design or not.

Returns:

TRUE if it has an array design, FALSE otherwise

getSpots

public int getSpots()

Deprecated. Use getNumDbSpots() or getNumFileSpots() instead. This method first checks the database and if not 0, it returns that value, otherwise it returns the number of file spots

Get the number of raw data spots that has been added to this raw bioassay.

Returns:

The number of spots

getNumDbSpots

public int getNumDbSpots()

Get the number of spots on this raw bioassay that are stored in the database.

Returns:

The number of spots in the database

Since:

2.5

getNumFileSpots

public int getNumFileSpots()

Get the number of spots on this raw bioassay that are stored inside files.

Returns:

The number of spots in files

Since:

2.5

setNumFileSpots

public void setNumFileSpots(int numSpots)

Set the number of spots that are stored in files.

Parameters:

numSpots - The number of spots

Since:

2.5

hasData

public boolean hasData()

If raw data has been added to this raw bioassay or not. Note that this method checks both data in the database and data in the form of files.

getSpotImages

public SpotImages getSpotImages()
                         throws PermissionDeniedException,
                                BaseException

Get the SpotImages item used to generate spot images for this raw bioassay. If no SpotImages exists a new one is created, and is automatically saved to the database (if commit is called).

Returns:

The SpotImages item

Throws:

PermissionDeniedException - If logged in user doesn't have read permission to the spot images.

BaseException - If there is some kind of error.

See Also:

hasSpotImages()

hasSpotImages

public boolean hasSpotImages()

Check if spot images exists for this raw bioassay or not.

See Also:

getSpotImages()

getHeader

public String getHeader(String name)

Get the value for the raw data header with the specified name.

Parameters:

name - The name of the header

Returns:

The value of the header or null if no header with that name exists

setHeader

public void setHeader(String name,
                      String value)
               throws PermissionDeniedException,
                      InvalidDataException

Set the value for a raw data header.

Parameters:

name - The name of the header

value - The value of the header

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or if spots already has been added to the raw bioassay

InvalidDataException - If the name or value is null or too long

removeHeaders

public void removeHeaders()

Remove all headers from the raw bioassay.

Since:

2.5

removeHeader

public void removeHeader(String name)

Remove a specific header from the raw bioassay.

Parameters:

name - The name of the header

Since:

2.5

getHeaderNames

public Set<String> getHeaderNames()

Get the names of all raw data headers. The set is sorted by name.

Returns:

A set containing the header names or an empty set if no headers have been defined

getExperiments

public ItemQuery<Experiment> getExperiments()

Get a query that returns all experiments where this raw bioassay is used.

Returns:

An ItemQuery object

getRawDataBatcher

public RawDataBatcher getRawDataBatcher()
                                 throws PermissionDeniedException,
                                        BaseException

Deprecated. Use getRawDataBatcher(FeatureIdentificationMethod, Job) instead

Throws:

PermissionDeniedException

BaseException

getRawDataBatcher

public RawDataBatcher getRawDataBatcher(FeatureIdentificationMethod fiMethod)
                                 throws PermissionDeniedException,
                                        BaseException

Deprecated. Use getRawDataBatcher(FeatureIdentificationMethod, Job) instead.

Throws:

PermissionDeniedException

BaseException

Since:

2.6

getRawDataBatcher

public RawDataBatcher getRawDataBatcher(FeatureIdentificationMethod fiMethod,
                                        Job job)
                                 throws PermissionDeniedException,
                                        BaseException

Get a raw data batcher object which can be used to add raw data to the raw bioassay.

Parameters:

fiMethod - The method to use for identifying features, or null to use the method choosen by the array design. This parameter has no meaning if the raw bioassay is not connected to an array design or if the array design has no features.

job - The job that is currently running, or null if the raw data import is not running as a job

Returns:

A RawDataBatcher object. If this method is called multiple times the fiMethod and job parameter is ignored and the same batcher as before is returned

Throws:

PermissionDeniedException - If raw data has already been added or the logged in user doesn't have write permission

BaseException - If there is another error

Since:

2.7

deleteRawData

public void deleteRawData()
                   throws PermissionDeniedException,
                          BaseException

Delete the raw data that has been added to the database for this raw bioassay. You should not call this method in the same transaction as adding raw data with the batcher from getRawDataBatcher().

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission or a RawDataBatcher has been fetched using the getRawDataBatcher() method or the raw bioassay is used by some experiment

BaseException - If there is another error

getRawDataById

public RawData getRawDataById(int id)
                       throws ItemNotFoundException,
                              BaseException

Get a raw data spot when you know the id. NOTE! This method may return an uninitialized proxy. If an initialized object is required use getRawDataById(int, boolean) instead.

Parameters:

id - The id of the spot

Returns:

An RawData object

Throws:

ItemNotFoundException - If no raw data item was found for the given id.

BaseException - If there some other error.

getRawDataById

public RawData getRawDataById(int id,
                              boolean forceInitialization)
                       throws ItemNotFoundException,
                              BaseException

Get a raw data spot when you know the id.

Parameters:

id - The id of the spot

forceInitialization - If TRUE the raw data and associated feature and reporter are sure to be initialized

Returns:

An RawData object

Throws:

ItemNotFoundException - If no raw data item was found for the given id.

BaseException - If there some other error.

Since:

2.15

getRawData

public DataQuery<RawData> getRawData()

Get a query that returns the raw data of this raw bioassay.

Returns:

A DataQuery object

getReporters

public DataQuery<ReporterData> getReporters()

Get a query that returns the reporters on this raw bioassay. The query is rooted at the raw data, which means that:

• All filters, sorting, etc. that works for getRawData() can be used without modifications on this query.
• The same reporter may be returned multiple times if it is present on multiple spots.
• 'Null' values may be returned if there are spots without a reporter

Returns:

A DataQuery object

Since:

2.8

getDynamicRawData

public DynamicRawDataQuery getDynamicRawData()

Get a dynamic query that returns the raw data of this raw bioassay.

Returns:

A DynamicRawDataQuery object

validateFeatures

private void validateFeatures(DbControl dc,
                              ArrayDesign design,
                              FeatureIdentificationMethod fiMethod,
                              boolean update,
                              ProgressReporter progress)

Validate that the features/reporters of the raw data matches the features/reporter on the array design.

Parameters:

dc - The DbControl to use for database access

design - The array design to validate against

fiMethod - The method to use for identifying features, or null to use the method choosen by the array design

update - If the raw data should be linked to the new feature or not

progress - An optional progress reporter

Since:

2.6