3.2.4: 2013-12-06

net.sf.basedb.core.data
Class DerivedBioAssayData

java.lang.Object
  extended by net.sf.basedb.core.data.BasicData
      extended by net.sf.basedb.core.data.OwnedData
          extended by net.sf.basedb.core.data.SharedData
              extended by net.sf.basedb.core.data.CommonData
                  extended by net.sf.basedb.core.data.AnnotatedData
                      extended by net.sf.basedb.core.data.DerivedBioAssayData
All Implemented Interfaces:
AnnotatableData, FileStoreEnabledData, IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData, SubtypableData

public class DerivedBioAssayData
extends AnnotatedData
implements RegisteredData, FileStoreEnabledData, SubtypableData

Since:
3.0
Author:
Nicklas
See Also:
Developer documentation: Bioassays and raw data
Last modified
$Date: 2012-08-17 14:04:45 +0200 (Fri, 17 Aug 2012) $
Hibernate: class
table="`DerivedBioAssays`" lazy="true"

Field Summary
private  Set<DerivedBioAssayData> children
           
private  Date entryDate
           
private  ExtractData extract
           
private  FileSetData fileSet
           
private  HardwareData hardware
           
private  boolean isRoot
           
private  JobData job
           
private  Set<DerivedBioAssayData> parents
           
private  Set<PhysicalBioAssayData> physicalBioAssays
           
private  ProtocolData protocol
           
private  Set<RawBioAssayData> rawBioAssays
           
private  SoftwareData software
           
private  ItemSubtypeData subtype
           
 
Fields inherited from interface net.sf.basedb.core.data.NameableData
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
 
Constructor Summary
DerivedBioAssayData()
           
 
Method Summary
 Set<DerivedBioAssayData> getChildren()
          This is the inverse end.
 Date getEntryDate()
          Get the date this item was added to the database.
 ExtractData getExtract()
          Get the extract that this bioassay is related to.
 FileSetData getFileSet()
          Get the file set attached to this item.
 HardwareData getHardware()
          Get the hardware used to create this bioassay set.
 ItemSubtypeData getItemSubtype()
          Get the subtype of the item.
 JobData getJob()
          Get the job used to create this bioassay set.
 Set<DerivedBioAssayData> getParents()
          A set that manages the parent bioassays that this derived bioassay related to.
 Set<PhysicalBioAssayData> getPhysicalBioAssays()
          A set that manages the parent physical bioassays that this derived bioassay is related to.
 ProtocolData getProtocol()
          Get the protocol used to create this bioassay set.
(package private)  Set<RawBioAssayData> getRawBioAssays()
          This is the inverse end.
 SoftwareData getSoftware()
          Get the software used to create this bioassay set.
 boolean isRoot()
          A flag indicating if this is a root derived bioassay or not.
(package private)  void setChildren(Set<DerivedBioAssayData> children)
           
 void setEntryDate(Date entryDate)
           
 void setExtract(ExtractData extract)
           
 void setFileSet(FileSetData fileSet)
          Attach a file set to the item.
 void setHardware(HardwareData hardware)
           
 void setItemSubtype(ItemSubtypeData subtype)
          Set the subtype of the item.
 void setJob(JobData job)
           
(package private)  void setParents(Set<DerivedBioAssayData> parents)
           
(package private)  void setPhysicalBioAssays(Set<PhysicalBioAssayData> physicalBioAssays)
           
 void setProtocol(ProtocolData protocol)
           
(package private)  void setRawBioAssays(Set<RawBioAssayData> rawBioAssays)
           
 void setRoot(boolean isRoot)
           
 void setSoftware(SoftwareData software)
           
 
Methods inherited from class net.sf.basedb.core.data.AnnotatedData
getAnnotations, getAnnotationSet, setAnnotations, setAnnotationSet
 
Methods inherited from class net.sf.basedb.core.data.CommonData
getDescription, getName, isRemoved, setDescription, setName, setRemoved
 
Methods inherited from class net.sf.basedb.core.data.SharedData
getItemKey, getProjectKey, setItemKey, setProjectKey
 
Methods inherited from class net.sf.basedb.core.data.OwnedData
getOwner, setOwner
 
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
 
Methods inherited from interface net.sf.basedb.core.data.OwnableData
getOwner, setOwner
 

Field Detail

subtype

private ItemSubtypeData subtype

fileSet

private FileSetData fileSet

entryDate

private Date entryDate

isRoot

private boolean isRoot

physicalBioAssays

private Set<PhysicalBioAssayData> physicalBioAssays

parents

private Set<DerivedBioAssayData> parents

children

private Set<DerivedBioAssayData> children

rawBioAssays

private Set<RawBioAssayData> rawBioAssays

protocol

private ProtocolData protocol

hardware

private HardwareData hardware

software

private SoftwareData software

job

private JobData job

extract

private ExtractData extract
Constructor Detail

DerivedBioAssayData

public DerivedBioAssayData()
Method Detail

getItemSubtype

public ItemSubtypeData getItemSubtype()
Description copied from interface: SubtypableData
Get the subtype of the item.

Specified by:
getItemSubtype in interface SubtypableData

setItemSubtype

public void setItemSubtype(ItemSubtypeData subtype)
Description copied from interface: SubtypableData
Set the subtype of the item.

Specified by:
setItemSubtype in interface SubtypableData

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

getEntryDate

public Date getEntryDate()
Description copied from interface: RegisteredData
Get the date this item was added to the database. The value is generated at creation time and can't be modified later.

Specified by:
getEntryDate in interface RegisteredData

setEntryDate

public void setEntryDate(Date entryDate)

isRoot

public boolean isRoot()
A flag indicating if this is a root derived bioassay or not. A root bioassay can only have physical bioassays as parents, while a non-root bioassay only can have other derived bioassays as parents (but the physical bioassays collection should be automatically managed to reflect the parents of the parents, etc.)

Since:
3.2
Hibernate: property
column="`is_root`" type="boolean" not-null="true"

setRoot

public void setRoot(boolean isRoot)

getPhysicalBioAssays

public Set<PhysicalBioAssayData> getPhysicalBioAssays()
A set that manages the parent physical bioassays that this derived bioassay is related to.

Since:
3.2
Hibernate: set
table="`ParentPhysicalBioAssays`" lazy="true"
Hibernate: collection-key
column="`derivedbioassay_id`"
Hibernate: collection-many-to-many
column="`physicalbioassay_id`" class="net.sf.basedb.core.data.PhysicalBioAssayData"

setPhysicalBioAssays

void setPhysicalBioAssays(Set<PhysicalBioAssayData> physicalBioAssays)

getParents

public Set<DerivedBioAssayData> getParents()
A set that manages the parent bioassays that this derived bioassay related to.

Since:
3.2
Hibernate: set
table="`ParentDerivedBioAssays`" lazy="true"
Hibernate: collection-key
column="`derivedbioassay_id`"
Hibernate: collection-many-to-many
column="`parentbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData"

setParents

void setParents(Set<DerivedBioAssayData> parents)

getChildren

public Set<DerivedBioAssayData> getChildren()
This is the inverse end.

See Also:
getParents()
Hibernate: set
table="`ParentDerivedBioAssays`" lazy="true" inverse="true"
Hibernate: collection-key
column="`parentbioassay_id`"
Hibernate: collection-many-to-many
column="`derivedbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData"

setChildren

void setChildren(Set<DerivedBioAssayData> children)

getRawBioAssays

Set<RawBioAssayData> getRawBioAssays()
This is the inverse end.

See Also:
RawBioAssayData.getParentBioAssay()
Hibernate: set
lazy="true" inverse="true"
Hibernate: collection-key
column="`bioassay_id`"
Hibernate: collection-one-to-many
class="net.sf.basedb.core.data.RawBioAssayData"

setRawBioAssays

void setRawBioAssays(Set<RawBioAssayData> rawBioAssays)

getProtocol

public ProtocolData getProtocol()
Get the protocol used to create this bioassay set.

Hibernate: many-to-one
column="`protocol_id`" not-null="false" outer-join="false"

setProtocol

public void setProtocol(ProtocolData protocol)

getHardware

public HardwareData getHardware()
Get the hardware used to create this bioassay set.

Hibernate: many-to-one
column="`hardware_id`" not-null="false" outer-join="false"

setHardware

public void setHardware(HardwareData hardware)

getSoftware

public SoftwareData getSoftware()
Get the software used to create this bioassay set.

Hibernate: many-to-one
column="`software_id`" not-null="false" outer-join="false"

setSoftware

public void setSoftware(SoftwareData software)

getJob

public JobData getJob()
Get the job used to create this bioassay set.

Hibernate: many-to-one
column="`job_id`" not-null="false" update="false" outer-join="false"

setJob

public void setJob(JobData job)

getExtract

public ExtractData getExtract()
Get the extract that this bioassay is related to.

Hibernate: many-to-one
column="`extract_id`" not-null="false" outer-join="false"

setExtract

public void setExtract(ExtractData extract)

3.2.4: 2013-12-06