net.sf.basedb.core.data
Class BioAssayData

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

All Implemented Interfaces:

AnnotatableData, IdentifiableData, NameableData

public class BioAssayData
extends BasicData
implements NameableData, AnnotatableData

This class holds information about a bioassay.

Version:

2.0

Author:

Nicklas

See Also:

BioAssay, Developer documentation: Experiments and analysis

Last modified

$Date: 2011-10-21 13:15:41 +0200 (Fri, 21 Oct 2011) $

Hibernate: class

table="`BioAssays`" lazy="true"

Field Summary

private AnnotationSetData	annotationSet
private BioAssaySetData	bioAssaySet
private Set<BioAssayData>	children
private DataCubeColumnData	dataCubeColumn
private String	description
private String	name
private int	numFileSpots
private int	numSpots
private Set<BioAssayData>	parents
private Set<RawBioAssayData>	rawParents

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioAssayData()

Method Summary

AnnotationSetData	getAnnotationSet() Get the annotation set that holds the annotations for an item.
BioAssaySetData	getBioAssaySet() Get the bioassayset this bioassay belongs to.
(package private) Set<BioAssayData>	getChildren() This is the inverse end to getParents().
DataCubeColumnData	getDataCubeColumn() Get the column this bioassay stores it's data in.
String	getDescription() Get the description for the item.
String	getName() Get the name of the item.
int	getNumFileSpots() The number of unique spots in this bioassayset.
int	getNumSpots() The number of unique spots in this bioassay.
Set<BioAssayData>	getParents() Get a set that manages the parent bioassays the data in this bioassay is based on.
Set<RawBioAssayData>	getRawParents() Get a set that manages the raw parent bioassays the data in this bioassay is based on.
void	setAnnotationSet(AnnotationSetData annotationSet) Change the annotation set.
void	setBioAssaySet(BioAssaySetData bioAssaySet)
(package private) void	setChildren(Set<BioAssayData> children)
void	setDataCubeColumn(DataCubeColumnData dataCubeColumn)
void	setDescription(String description) Set the description for the item.
void	setName(String name) Set the name of the item.
void	setNumFileSpots(int numFileSpots)
void	setNumSpots(int numSpots)
(package private) void	setParents(Set<BioAssayData> parents)
(package private) void	setRawParents(Set<RawBioAssayData> rawParents)

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

annotationSet

private AnnotationSetData annotationSet

bioAssaySet

private BioAssaySetData bioAssaySet

dataCubeColumn

private DataCubeColumnData dataCubeColumn

numSpots

private int numSpots

numFileSpots

private int numFileSpots

parents

private Set<BioAssayData> parents

children

private Set<BioAssayData> children

rawParents

private Set<RawBioAssayData> rawParents

Constructor Detail

BioAssayData

public BioAssayData()

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

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

getBioAssaySet

public BioAssaySetData getBioAssaySet()

Get the bioassayset this bioassay belongs to.

Hibernate: many-to-one

column="`bioassayset_id`" not-null="true" outer-join="false" update="false" unique-key="uniquecolumn"

setBioAssaySet

public void setBioAssaySet(BioAssaySetData bioAssaySet)

getDataCubeColumn

public DataCubeColumnData getDataCubeColumn()

Get the column this bioassay stores it's data in.

Hibernate: many-to-one

column="`datacubecolumn_id`" not-null="true" unique-key="uniquecolumn" outer-join="false" update="false" cascade="save-update"

setDataCubeColumn

public void setDataCubeColumn(DataCubeColumnData dataCubeColumn)

getNumSpots

public int getNumSpots()

The number of unique spots in this bioassay.

Hibernate: property

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

setNumSpots

public void setNumSpots(int numSpots)

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

getParents

public Set<BioAssayData> getParents()

Get a set that manages the parent bioassays the data in this bioassay is based on.

Hibernate: set

table="`BioAssayParents`" lazy="true"

Hibernate: collection-key

column="`bioassay_id`"

Hibernate: collection-many-to-many

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

setParents

void setParents(Set<BioAssayData> parents)

getChildren

Set<BioAssayData> getChildren()

This is the inverse end to getParents().

Hibernate: set

table="`BioAssayParents`" 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"

setChildren

void setChildren(Set<BioAssayData> children)

getRawParents

public Set<RawBioAssayData> getRawParents()

Get a set that manages the raw parent bioassays the data in this bioassay is based on.

Hibernate: set

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

Hibernate: collection-key

column="`bioassay_id`"

Hibernate: collection-many-to-many

column="`parent_id`" class="net.sf.basedb.core.data.RawBioAssayData"

setRawParents

void setRawParents(Set<RawBioAssayData> rawParents)