Package net.sf.basedb.core.data
Class BioAssayData
- java.lang.Object
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- net.sf.basedb.core.data.BasicData
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- net.sf.basedb.core.data.BioAssayData
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- 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: 2016-04-27 08:38:21 +0200 (on, 27 apr 2016) $
- Hibernate: class
- table="`BioAssays`" lazy="true"
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Field Summary
Fields Modifier and Type Field Description private AnnotationSetData
annotationSet
private BioAssaySetData
bioAssaySet
private Set<BioAssayData>
children
private DataCubeColumnData
dataCubeColumn
private String
description
private Set<AnnotationLink>
links
private String
name
private int
numFileSpots
private int
numSpots
private Set<BioAssayData>
parents
private Set<RawBioAssayData>
rawParents
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Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
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Constructor Summary
Constructors Constructor Description BioAssayData()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Set<AnnotationLink>
getAnnotations()
Short-cut to all annotations belonging to this item.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 togetParents()
.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.(package private) void
setAnnotations(Set<AnnotationLink> links)
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)
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Methods inherited from class net.sf.basedb.core.data.BasicData
equals, getId, getVersion, hashCode, setId, setVersion, toString
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.data.IdentifiableData
getId, getVersion
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Field Detail
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name
private String name
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description
private String description
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annotationSet
private AnnotationSetData annotationSet
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links
private Set<AnnotationLink> links
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bioAssaySet
private BioAssaySetData bioAssaySet
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dataCubeColumn
private DataCubeColumnData dataCubeColumn
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numSpots
private int numSpots
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numFileSpots
private int numFileSpots
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parents
private Set<BioAssayData> parents
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children
private Set<BioAssayData> children
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rawParents
private Set<RawBioAssayData> rawParents
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Method Detail
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getName
public String getName()
Description copied from interface:NameableData
Get the name of the item.- Specified by:
getName
in interfaceNameableData
- Returns:
- A
String
with the name of the item
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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 theMAX_NAME_LENGTH
constant.- Specified by:
setName
in interfaceNameableData
- Parameters:
name
- The new name for the item
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getDescription
public String getDescription()
Description copied from interface:NameableData
Get the description for the item.- Specified by:
getDescription
in interfaceNameableData
- Returns:
- A
String
with a description of the item
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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 theMAX_DESCRIPTION_LENGTH
constant.- Specified by:
setDescription
in interfaceNameableData
- Parameters:
description
- The new description for the item
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getAnnotationSet
public AnnotationSetData getAnnotationSet()
Description copied from interface:AnnotatableData
Get the annotation set that holds the annotations for an item.- Specified by:
getAnnotationSet
in interfaceAnnotatableData
- Returns:
- An
AnnotationSetData
item or null if no annotations exist - Since:
- 2.2
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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 interfaceAnnotatableData
- Parameters:
annotationSet
- Annotation set to change to.- Since:
- 2.2
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getAnnotations
public Set<AnnotationLink> getAnnotations()
Description copied from interface:AnnotatableData
Short-cut to all annotations belonging to this item. Used for HQL queries only. This is the inverse end. NOTE! The property-ref="annotationSet" require that AnnotationSetData implements Serializable- Specified by:
getAnnotations
in interfaceAnnotatableData
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setAnnotations
void setAnnotations(Set<AnnotationLink> links)
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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="BioAssay_uniquecolumn"
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setBioAssaySet
public void setBioAssaySet(BioAssaySetData bioAssaySet)
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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="BioAssay_uniquecolumn" outer-join="false" update="false" cascade="save-update"
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setDataCubeColumn
public void setDataCubeColumn(DataCubeColumnData dataCubeColumn)
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getNumSpots
public int getNumSpots()
The number of unique spots in this bioassay.- Hibernate: property
- column="`spots`" type="int" not-null="true" update="false"
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setNumSpots
public void setNumSpots(int numSpots)
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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"
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setNumFileSpots
public void setNumFileSpots(int numFileSpots)
- Since:
- 2.8
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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"
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setParents
void setParents(Set<BioAssayData> parents)
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getChildren
Set<BioAssayData> getChildren()
This is the inverse end togetParents()
.- 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"
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setChildren
void setChildren(Set<BioAssayData> children)
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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"
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setRawParents
void setRawParents(Set<RawBioAssayData> rawParents)
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