net.sf.basedb.core.data
Class BioAssaySetData

java.lang.Object
  net.sf.basedb.core.data.BasicData
      net.sf.basedb.core.data.BioAssaySetData

All Implemented Interfaces:

AnnotatableData, FileStoreEnabledData, IdentifiableData, NameableData, RemovableData

public class BioAssaySetData
extends BasicData
implements NameableData, RemovableData, AnnotatableData, FileStoreEnabledData

This class holds information about a bioassayset.

Version:

2.0

Author:

Nicklas

See Also:

BioAssaySet, Experiments and analysis overview

Last modified

$Date: 2009-04-29 11:05:20 +0200 (Wed, 29 Apr 2009) $

Hibernate: class

table="`BioAssaySets`" lazy="true"

Field Summary

private AnnotationSetData	annotationSet
private Set<BioAssayData>	bioAssays
private DataCubeFilterData	dataCubeFilter
private DataCubeLayerData	dataCubeLayer
private String	description
private ExperimentData	experiment
private Map<ExtraValueTypeData,ExtraValueData>	extraValues
private FileSetData	fileSet
private int	intensityTransform
private String	name
private int	numFileReporters
private int	numFileSpots
private int	numReporters
private int	numSpots
private boolean	removed
private TransformationData	transformation
private Set<TransformationData>	transformations

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioAssaySetData()

Method Summary

AnnotationSetData	getAnnotationSet() Get the annotation set that holds the annotations for an item.
(package private) Set<BioAssayData>	getBioAssays() This is the inverse end.
DataCubeFilterData	getDataCubeFilter() Get the filter used by this bioassayset.
DataCubeLayerData	getDataCubeLayer() Get the layer this bioassayset stores it's data in.
String	getDescription() Get the description for the item.
ExperimentData	getExperiment() Get the experiment this bioassayset belongs to.
Map<ExtraValueTypeData,ExtraValueData>	getExtraValues() The extra values calculated for this bioassayset.
FileSetData	getFileSet() Get the file set attached to this item.
int	getIntensityTransform() A flag indicating how the spot intensities has been transformed before it was stored in the database: 0 = no transformation; 1 = 2-log; 2 = 10-log
String	getName() Get the name of the item.
int	getNumFileReporters() The number of unique reporters as stored in files in this bioassayset.
int	getNumFileSpots() The number of unique spots in this bioassayset.
int	getNumReporters() The number of unique reporters in this bioassayset.
int	getNumSpots() The number of unique spots in this bioassayset.
TransformationData	getTransformation() Get the transformation that created this bioassayset.
(package private) Set<TransformationData>	getTransformations() This is the inverse end.
boolean	isRemoved() Check if the removed flag is set for this item.
void	setAnnotationSet(AnnotationSetData annotationSet) Change the annotation set.
(package private) void	setBioAssays(Set<BioAssayData> bioAssays)
void	setDataCubeFilter(DataCubeFilterData dataCubeFilter)
void	setDataCubeLayer(DataCubeLayerData dataCubeLayer)
void	setDescription(String description) Set the description for the item.
void	setExperiment(ExperimentData experiment)
(package private) void	setExtraValues(Map<ExtraValueTypeData,ExtraValueData> extraValues)
void	setFileSet(FileSetData fileSet) Attach a file set to the item.
void	setIntensityTransform(int intensityTransform)
void	setName(String name) Set the name of the item.
void	setNumFileReporters(int numFileReporters)
void	setNumFileSpots(int numFileSpots)
void	setNumReporters(int numReporters)
void	setNumSpots(int numSpots)
void	setRemoved(boolean removed) Set the removed flag for this item.
void	setTransformation(TransformationData transformation)
(package private) void	setTransformations(Set<TransformationData> transformations)

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.IdentifiableData

getId, getVersion

Field Detail

name

private String name

description

private String description

removed

private boolean removed

annotationSet

private AnnotationSetData annotationSet

fileSet

private FileSetData fileSet

experiment

private ExperimentData experiment

transformation

private TransformationData transformation

dataCubeLayer

private DataCubeLayerData dataCubeLayer

dataCubeFilter

private DataCubeFilterData dataCubeFilter

numReporters

private int numReporters

numSpots

private int numSpots

numFileReporters

private int numFileReporters

numFileSpots

private int numFileSpots

bioAssays

private Set<BioAssayData> bioAssays

transformations

private Set<TransformationData> transformations

extraValues

private Map<ExtraValueTypeData,ExtraValueData> extraValues

intensityTransform

private int intensityTransform

Constructor Detail

BioAssaySetData

public BioAssaySetData()

Method Detail

getName

public String getName()

Description copied from interface: NameableData

Get the name of the item.

Specified by:

getName in interface NameableData

Returns:

A String with the name of the item

setName

public void setName(String name)

Description copied from interface: NameableData

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

Specified by:

setName in interface NameableData

Parameters:

name - The new name for the item

getDescription

public String getDescription()

Description copied from interface: NameableData

Get the description for the item.

Specified by:

getDescription in interface NameableData

Returns:

A String with a description of the item

setDescription

public void setDescription(String description)

Description copied from interface: NameableData

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

Specified by:

setDescription in interface NameableData

Parameters:

description - The new description for the item

isRemoved

public boolean isRemoved()

Description copied from interface: RemovableData

Check if the removed flag is set for this item.

Specified by:

isRemoved in interface RemovableData

Returns:

TRUE if the item is flagged as removed, FALSE otherwise

setRemoved

public void setRemoved(boolean removed)

Description copied from interface: RemovableData

Set the removed flag for this item.

Specified by:

setRemoved in interface RemovableData

Parameters:

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

getAnnotationSet

public AnnotationSetData getAnnotationSet()

Description copied from interface: AnnotatableData

Get the annotation set that holds the annotations for an item.

Specified by:

getAnnotationSet in interface AnnotatableData

Returns:

An AnnotationSetData item or null if no annotations exist

Since:

2.2

setAnnotationSet

public void setAnnotationSet(AnnotationSetData annotationSet)

Description copied from interface: AnnotatableData

Change the annotation set. Use null to remove the annotations.

Specified by:

setAnnotationSet in interface AnnotatableData

Parameters:

annotationSet - Annotation set to change to.

Since:

2.2

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

getExperiment

public ExperimentData getExperiment()

Get the experiment this bioassayset belongs to.

Hibernate: many-to-one

column="`experiment_id`" not-null="true" outer-join="false" update="false"

setExperiment

public void setExperiment(ExperimentData experiment)

getTransformation

public TransformationData getTransformation()

Get the transformation that created this bioassayset.

Hibernate: many-to-one

column="`transformation_id`" not-null="true" outer-join="false" update="false"

setTransformation

public void setTransformation(TransformationData transformation)

getDataCubeLayer

public DataCubeLayerData getDataCubeLayer()

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

Hibernate: many-to-one

column="`datacubelayer_id`" not-null="true" outer-join="false" update="false"

setDataCubeLayer

public void setDataCubeLayer(DataCubeLayerData dataCubeLayer)

getDataCubeFilter

public DataCubeFilterData getDataCubeFilter()

Get the filter used by this bioassayset. Null = no filter

Hibernate: many-to-one

column="`datacubefilter_id`" not-null="false" outer-join="false" update="false" cascade="save-update"

setDataCubeFilter

public void setDataCubeFilter(DataCubeFilterData dataCubeFilter)

getNumReporters

public int getNumReporters()

The number of unique reporters in this bioassayset.

Hibernate: property

column="`reporters`" type="int" not-null="true" update="false"

setNumReporters

public void setNumReporters(int numReporters)

getNumSpots

public int getNumSpots()

The number of unique spots in this bioassayset.

Hibernate: property

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

setNumSpots

public void setNumSpots(int numSpots)

getNumFileReporters

public int getNumFileReporters()

The number of unique reporters as stored in files in this bioassayset.

Since:

2.8

Hibernate: property

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

setNumFileReporters

public void setNumFileReporters(int numFileReporters)

Since:

2.8

getNumFileSpots

public int getNumFileSpots()

The number of unique spots in this bioassayset.

Since:

2.8

Hibernate: property

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

setNumFileSpots

public void setNumFileSpots(int numFileSpots)

Since:

2.8

getBioAssays

Set<BioAssayData> getBioAssays()

This is the inverse end.

See Also:

BioAssayData.getBioAssaySet()

Hibernate: set

lazy="true" inverse="true" cascade="delete"

Hibernate: collection-key

column="`bioassayset_id`"

Hibernate: collection-one-to-many

class="net.sf.basedb.core.data.BioAssayData"

setBioAssays

void setBioAssays(Set<BioAssayData> bioAssays)

getTransformations

Set<TransformationData> getTransformations()

This is the inverse end.

See Also:

TransformationData.getSource()

Hibernate: set

lazy="true" inverse="true" cascade="delete"

Hibernate: collection-key

column="`bioassayset_id`"

Hibernate: collection-one-to-many

class="net.sf.basedb.core.data.TransformationData"

setTransformations

void setTransformations(Set<TransformationData> transformations)

getExtraValues

public Map<ExtraValueTypeData,ExtraValueData> getExtraValues()

The extra values calculated for this bioassayset. This is the inverse end. This method is public since we need it for reading extra values from the bioassayset. The map should never be modified by the core.

See Also:

ExtraValueData.getBioAssaySet(), ExtraValueData.getExtraValueType()

Hibernate: map

lazy="true" cascade="all" inverse="true"

Hibernate: index-many-to-many

column="`extravaluetype_id`" class="net.sf.basedb.core.data.ExtraValueTypeData"

Hibernate: collection-key

column="`bioassayset_id`"

Hibernate: collection-one-to-many

column="`extravalue_id`" class="net.sf.basedb.core.data.ExtraValueData"

setExtraValues

void setExtraValues(Map<ExtraValueTypeData,ExtraValueData> extraValues)

getIntensityTransform

public int getIntensityTransform()

A flag indicating how the spot intensities has been transformed before it was stored in the database: 0 = no transformation; 1 = 2-log; 2 = 10-log

Since:

2.12

Hibernate: property

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

setIntensityTransform

public void setIntensityTransform(int intensityTransform)

Since:

2.12