Package net.sf.basedb.core.data
Class BioAssaySetData
- java.lang.Object
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- net.sf.basedb.core.data.BasicData
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- net.sf.basedb.core.data.BioAssaySetData
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- 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
, Developer documentation: Experiments and analysis- Last modified
- $Date: 2016-04-27 08:38:21 +0200 (on, 27 apr 2016) $
- Hibernate: class
- table="`BioAssaySets`" lazy="true"
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Field Summary
Fields Modifier and Type Field Description 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 Set<AnnotationLink>
links
private String
name
private int
numFileReporters
private int
numFileSpots
private int
numReporters
private int
numSpots
private Integer
removedBy
private TransformationData
transformation
private Set<TransformationData>
transformations
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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 BioAssaySetData()
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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.(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-logString
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.Integer
getRemovedBy()
Get the ID of the user that removed this item.TransformationData
getTransformation()
Get the transformation that created this bioassayset.(package private) Set<TransformationData>
getTransformations()
This is the inverse end.(package private) void
setAnnotations(Set<AnnotationLink> links)
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
setRemovedBy(Integer removedBy)
Set the ID of the user that removed this item or null to restore the item.void
setTransformation(TransformationData transformation)
(package private) void
setTransformations(Set<TransformationData> transformations)
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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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removedBy
private Integer removedBy
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annotationSet
private AnnotationSetData annotationSet
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links
private Set<AnnotationLink> links
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fileSet
private FileSetData fileSet
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experiment
private ExperimentData experiment
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transformation
private TransformationData transformation
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dataCubeLayer
private DataCubeLayerData dataCubeLayer
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dataCubeFilter
private DataCubeFilterData dataCubeFilter
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numReporters
private int numReporters
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numSpots
private int numSpots
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numFileReporters
private int numFileReporters
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numFileSpots
private int numFileSpots
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bioAssays
private Set<BioAssayData> bioAssays
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transformations
private Set<TransformationData> transformations
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extraValues
private Map<ExtraValueTypeData,ExtraValueData> extraValues
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intensityTransform
private int intensityTransform
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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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getRemovedBy
public Integer getRemovedBy()
Description copied from interface:RemovableData
Get the ID of the user that removed this item.- Specified by:
getRemovedBy
in interfaceRemovableData
- Returns:
- The ID of a user or null if the item is not removed
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setRemovedBy
public void setRemovedBy(Integer removedBy)
Description copied from interface:RemovableData
Set the ID of the user that removed this item or null to restore the item.- Specified by:
setRemovedBy
in interfaceRemovableData
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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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getFileSet
public FileSetData getFileSet()
Description copied from interface:FileStoreEnabledData
Get the file set attached to this item.- Specified by:
getFileSet
in interfaceFileStoreEnabledData
- Returns:
- A
FileSetData
object or null if no files are attached
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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 interfaceFileStoreEnabledData
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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"
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setExperiment
public void setExperiment(ExperimentData experiment)
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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"
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setTransformation
public void setTransformation(TransformationData transformation)
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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"
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setDataCubeLayer
public void setDataCubeLayer(DataCubeLayerData dataCubeLayer)
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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"
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setDataCubeFilter
public void setDataCubeFilter(DataCubeFilterData dataCubeFilter)
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getNumReporters
public int getNumReporters()
The number of unique reporters in this bioassayset.- Hibernate: property
- column="`reporters`" type="int" not-null="true" update="false"
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setNumReporters
public void setNumReporters(int numReporters)
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getNumSpots
public int getNumSpots()
The number of unique spots in this bioassayset.- 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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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"
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setNumFileReporters
public void setNumFileReporters(int numFileReporters)
- Since:
- 2.8
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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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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"
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setBioAssays
void setBioAssays(Set<BioAssayData> bioAssays)
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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"
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setTransformations
void setTransformations(Set<TransformationData> transformations)
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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"
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setExtraValues
void setExtraValues(Map<ExtraValueTypeData,ExtraValueData> extraValues)
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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"
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setIntensityTransform
public void setIntensityTransform(int intensityTransform)
- Since:
- 2.12
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