net.sf.basedb.core.data
Class RawBioAssayData

java.lang.Object
  net.sf.basedb.core.data.BasicData
      net.sf.basedb.core.data.OwnedData
          net.sf.basedb.core.data.SharedData
              net.sf.basedb.core.data.CommonData
                  net.sf.basedb.core.data.AnnotatedData
                      net.sf.basedb.core.data.RawBioAssayData

All Implemented Interfaces:

AnnotatableData, DiskConsumableData, FileStoreEnabledData, IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData

public class RawBioAssayData
extends AnnotatedData
implements DiskConsumableData, FileStoreEnabledData, RegisteredData

This class holds information about a raw bioassay, which is the raw data extracted from a scan.

Version:

2.0

Author:

Nicklas

See Also:

RawBioAssay, Hybridzations and raw data overview

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Hibernate: class

table="`RawBioAssays`" lazy="true"

Field Summary

private ArrayDesignData	arrayDesign
private int	arrayNum
private Set<BioAssayData>	bioAssays
private long	bytes
private DiskUsageData	diskUsage
private Date	entryDate
private Set<ExperimentData>	experiments
private FileSetData	fileSet
private int	fileSpots
private boolean	hasData
private Map<String,String>	headers
private JobData	job
static int	MAX_HEADER_NAME_LENGTH
static int	MAX_HEADER_VALUE_LENGTH
private PlatformData	platform
private ProtocolData	protocol
private String	rawDataType
private ScanData	scan
private SoftwareData	software
private SpotImagesData	spotImages
private int	spots
private Set<TransformationData>	transformations
private PlatformVariantData	variant

Fields inherited from interface net.sf.basedb.core.data.NameableData

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

RawBioAssayData()

Method Summary

ArrayDesignData	getArrayDesign() Get the array design used for the hybridization this raw bio assay comes from.
int	getArrayNum() The array number this raw bioassay is linked to on a multi-array hybridization.
(package private) Set<BioAssayData>	getBioAssays() This is the inverse end.
long	getBytes() The number of bytes the raw data occupies on disk.
DiskUsageData	getDiskUsage() Get the DiskUsageData that this item use.
Date	getEntryDate() Get the date this item was added to the database.
(package private) Set<ExperimentData>	getExperiments() This is the inverse end.
FileSetData	getFileSet() Get the file set attached to this item.
boolean	getHasData() If the raw bioassay has data or not.
Map<String,String>	getHeaders() File headers from the raw data file.
JobData	getJob() Get the job that was used to import raw data to this raw bioassay
int	getNumFileSpots() The number of spots on this raw bioassay that are stored inside files.
PlatformData	getPlatform() Get the platform this raw bioassay uses.
ProtocolData	getProtocol() Get the protocol used for the image analysis.
String	getRawDataType() Get the name of the raw data type used by this raw bio assay.
ScanData	getScan() Get the scan.
SoftwareData	getSoftware() Get the software used to analyse the scanned image and produce the raw data.
SpotImagesData	getSpotImages() Get the settings used for generating spot images for this raw bio assay.
int	getSpots() The number of data spots in this raw bio assay, that are stored in the database.
(package private) Set<TransformationData>	getTransformations() This is the inverse end.
PlatformVariantData	getVariant() Get the platform variant this raw bioassay uses, or null.
void	setArrayDesign(ArrayDesignData arrayDesign)
void	setArrayNum(int arrayNum)
(package private) void	setBioAssays(Set<BioAssayData> bioAssays)
void	setBytes(long bytes)
(package private) void	setDiskUsage(DiskUsageData diskUsage)
void	setEntryDate(Date entryDate)
(package private) void	setExperiments(Set<ExperimentData> experiments)
void	setFileSet(FileSetData fileSet) Attach a file set to the item.
void	setHasData(boolean hasData)
(package private) void	setHeaders(Map<String,String> headers)
void	setJob(JobData job)
void	setNumFileSpots(int fileSpots)
void	setPlatform(PlatformData platform)
void	setProtocol(ProtocolData protocol)
void	setRawDataType(String rawDataType)
void	setScan(ScanData scan)
void	setSoftware(SoftwareData software)
(package private) void	setSpotImages(SpotImagesData spotImages)
void	setSpots(int spots)
(package private) void	setTransformations(Set<TransformationData> transformations)
void	setVariant(PlatformVariantData variant)

Methods inherited from class net.sf.basedb.core.data.AnnotatedData

getAnnotationSet, setAnnotationSet

Methods inherited from class net.sf.basedb.core.data.CommonData

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class net.sf.basedb.core.data.SharedData

getItemKey, getProjectKey, setItemKey, setProjectKey

Methods inherited from class net.sf.basedb.core.data.OwnedData

getOwner, setOwner

Methods inherited from class net.sf.basedb.core.data.BasicData

equals, getId, getVersion, hashCode, setId, setVersion, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.data.OwnableData

getOwner, setOwner

Methods inherited from interface net.sf.basedb.core.data.IdentifiableData

getId, getVersion

Field Detail

diskUsage

private DiskUsageData diskUsage

fileSet

private FileSetData fileSet

entryDate

private Date entryDate

platform

private PlatformData platform

variant

private PlatformVariantData variant

job

private JobData job

arrayNum

private int arrayNum

scan

private ScanData scan

software

private SoftwareData software

protocol

private ProtocolData protocol

arrayDesign

private ArrayDesignData arrayDesign

spotImages

private SpotImagesData spotImages

rawDataType

private String rawDataType

hasData

private boolean hasData

spots

private int spots

fileSpots

private int fileSpots

bytes

private long bytes

MAX_HEADER_NAME_LENGTH

public static final int MAX_HEADER_NAME_LENGTH

See Also:

Constant Field Values

MAX_HEADER_VALUE_LENGTH

public static final int MAX_HEADER_VALUE_LENGTH

See Also:

Constant Field Values

headers

private Map<String,String> headers

experiments

private Set<ExperimentData> experiments

transformations

private Set<TransformationData> transformations

bioAssays

private Set<BioAssayData> bioAssays

Constructor Detail

RawBioAssayData

public RawBioAssayData()

Method Detail

getDiskUsage

public DiskUsageData getDiskUsage()

Description copied from interface: DiskConsumableData

Get the DiskUsageData that this item use.

Specified by:

getDiskUsage in interface DiskConsumableData

setDiskUsage

void setDiskUsage(DiskUsageData diskUsage)

getFileSet

public FileSetData getFileSet()

Description copied from interface: FileStoreEnabledData

Get the file set attached to this item.

Specified by:

getFileSet in interface FileStoreEnabledData

Returns:

A FileSetData object or null if no files are attached

setFileSet

public void setFileSet(FileSetData fileSet)

Description copied from interface: FileStoreEnabledData

Attach a file set to the item. Null is allowed to unlink it.

Specified by:

setFileSet in interface FileStoreEnabledData

getEntryDate

public Date getEntryDate()

Description copied from interface: RegisteredData

Get the date this item was added to the database. The value is generated at creation time and can't be modified later.

Specified by:

getEntryDate in interface RegisteredData

setEntryDate

public void setEntryDate(Date entryDate)

getPlatform

public PlatformData getPlatform()

Get the platform this raw bioassay uses.

Since:

2.5

Hibernate: column

name="`platform_id`" not-null="true"

Hibernate: many-to-one

outer-join="false"

setPlatform

public void setPlatform(PlatformData platform)

getVariant

public PlatformVariantData getVariant()

Get the platform variant this raw bioassay uses, or null.

Since:

2.5

Hibernate: column

name="`variant_id`"

Hibernate: many-to-one

outer-join="false"

setVariant

public void setVariant(PlatformVariantData variant)

getJob

public JobData getJob()

Get the job that was used to import raw data to this raw bioassay

Since:

2.7

Hibernate: many-to-one

column="`job_id`" not-null="false" outer-join="false"

setJob

public void setJob(JobData job)

Since:

2.7

getArrayNum

public int getArrayNum()

The array number this raw bioassay is linked to on a multi-array hybridization.

Since:

2.6

Hibernate: property

column="`array_num`" type="int" not-null="true"

setArrayNum

public void setArrayNum(int arrayNum)

getScan

public ScanData getScan()

Get the scan.

Hibernate: many-to-one

column="`scan_id`" not-null="false" outer-join="false"

setScan

public void setScan(ScanData scan)

getSoftware

public SoftwareData getSoftware()

Get the software used to analyse the scanned image and produce the raw data.

Hibernate: many-to-one

column="`software_id`" not-null="false" outer-join="false"

setSoftware

public void setSoftware(SoftwareData software)

getProtocol

public ProtocolData getProtocol()

Get the protocol used for the image analysis.

Hibernate: many-to-one

column="`protocol_id`" not-null="false" outer-join="false"

setProtocol

public void setProtocol(ProtocolData protocol)

getArrayDesign

public ArrayDesignData getArrayDesign()

Get the array design used for the hybridization this raw bio assay comes from.

Hibernate: many-to-one

column="`arraydesign_id`" not-null="false" outer-join="false"

setArrayDesign

public void setArrayDesign(ArrayDesignData arrayDesign)

getSpotImages

public SpotImagesData getSpotImages()

Get the settings used for generating spot images for this raw bio assay.

Hibernate: one-to-one

property-ref="rawBioAssay" cascade="delete"

setSpotImages

void setSpotImages(SpotImagesData spotImages)

getRawDataType

public String getRawDataType()

Get the name of the raw data type used by this raw bio assay.

Hibernate: property

column="`rawdatatype`" type="string" length="255" not-null="true"

setRawDataType

public void setRawDataType(String rawDataType)

getHasData

public boolean getHasData()

If the raw bioassay has data or not.

Hibernate: property

column="`has_data`" type="boolean" not-null="true"

setHasData

public void setHasData(boolean hasData)

getSpots

public int getSpots()

The number of data spots in this raw bio assay, that are stored in the database.

Since:

2.5

Hibernate: property

column="`spots`" type="int" not-null="true"

setSpots

public void setSpots(int spots)

getNumFileSpots

public int getNumFileSpots()

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

Since:

2.5

Hibernate: property

column="`file_spots`" type="int" not-null="true"

setNumFileSpots

public void setNumFileSpots(int fileSpots)

getBytes

public long getBytes()

The number of bytes the raw data occupies on disk.

Hibernate: property

column="`bytes`" type="long" not-null="true"

setBytes

public void setBytes(long bytes)

getHeaders

public Map<String,String> getHeaders()

File headers from the raw data file.

Hibernate: map

table="`RawBioAssayHeaders`" lazy="true" cascade="all"

Hibernate: collection-key

column="`rawbioassay_id`"

Hibernate: collection-index

column="`name`" type="string" length="255" not-null="true"

Hibernate: collection-element

column="`value`" type="text" not-null="true"

setHeaders

void setHeaders(Map<String,String> headers)

getExperiments

Set<ExperimentData> getExperiments()

This is the inverse end. We keep the inverse="true" attribute because we don't want to remove a raw bioassay that is used by an experiment.

See Also:

ExperimentData.getRawBioAssays()

Hibernate: set

table="`ExperimentRawBioAssays`" lazy="true" inverse="true"

Hibernate: collection-key

column="`rawbioassay_id`"

Hibernate: collection-many-to-many

column="`experiment_id`" class="net.sf.basedb.core.data.ExperimentData"

setExperiments

void setExperiments(Set<ExperimentData> experiments)

getTransformations

Set<TransformationData> getTransformations()

This is the inverse end. We keep the inverse="true" attribute because we don't want to remove a raw bioassay that is used by a transformation.

See Also:

TransformationData.getRawSources()

Hibernate: set

table="`TransformationRawBioAssays`" lazy="true" inverse="true"

Hibernate: collection-key

column="`rawbioassay_id`"

Hibernate: collection-many-to-many

column="`transformation_id`" class="net.sf.basedb.core.data.TransformationData"

setTransformations

void setTransformations(Set<TransformationData> transformations)

getBioAssays

Set<BioAssayData> getBioAssays()

This is the inverse end. We keep the inverse="true" attribute because we don't want to remove a raw bioassay that is used by a bioassay.

See Also:

BioAssayData.getRawParents()

Hibernate: set

table="`BioAssayRawParents`" lazy="true" inverse="true"

Hibernate: collection-key

column="`parent_id`"

Hibernate: collection-many-to-many

column="`bioassay_id`" class="net.sf.basedb.core.data.BioAssayData"

setBioAssays

void setBioAssays(Set<BioAssayData> bioAssays)