2.17.2: 2011-06-17

net.sf.basedb.core.data
Class BioAssaySetData

java.lang.Object
  extended by net.sf.basedb.core.data.BasicData
      extended by 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

2.17.2: 2011-06-17