Package 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:
- Last modified
- $Date: 2016-04-27 08:38:21 +0200 (on, 27 apr 2016) $
- Hibernate: class
- table="`BioAssaySets`" lazy="true"
-
Field Summary
Modifier and TypeFieldDescriptionprivate AnnotationSetData
private Set<BioAssayData>
private DataCubeFilterData
private DataCubeLayerData
private String
private ExperimentData
private Map<ExtraValueTypeData,
ExtraValueData> private FileSetData
private int
private Set<AnnotationLink>
private String
private int
private int
private int
private int
private Integer
private TransformationData
private Set<TransformationData>
Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionShort-cut to all annotations belonging to this item.Get the annotation set that holds the annotations for an item.(package private) Set<BioAssayData>
This is the inverse end.Get the filter used by this bioassayset.Get the layer this bioassayset stores it's data in.Get the description for the item.Get the experiment this bioassayset belongs to.The extra values calculated for this bioassayset.Get the file set attached to this item.int
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-loggetName()
Get the name of the item.int
The number of unique reporters as stored in files in this bioassayset.int
The number of unique spots in this bioassayset.int
The number of unique reporters in this bioassayset.int
The number of unique spots in this bioassayset.Get the ID of the user that removed this item.Get the transformation that created this bioassayset.(package private) Set<TransformationData>
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
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) 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
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Field Details
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name
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description
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removedBy
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annotationSet
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links
-
fileSet
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experiment
-
transformation
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dataCubeLayer
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dataCubeFilter
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numReporters
private int numReporters -
numSpots
private int numSpots -
numFileReporters
private int numFileReporters -
numFileSpots
private int numFileSpots -
bioAssays
-
transformations
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extraValues
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intensityTransform
private int intensityTransform
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Constructor Details
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BioAssaySetData
public BioAssaySetData()
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Method Details
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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
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
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
-
setDescription
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
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
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
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
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
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
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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
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
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
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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
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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
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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
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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) -
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) -
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:
- 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
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getTransformations
Set<TransformationData> getTransformations()This is the inverse end.- See Also:
- 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
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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:
- 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
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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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