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java.lang.Objectnet.sf.basedb.core.BasicItem<D>
net.sf.basedb.core.OwnedItem<D>
net.sf.basedb.core.SharedItem<D>
net.sf.basedb.core.CommonItem<D>
net.sf.basedb.core.AnnotatedItem<DerivedBioAssayData>
net.sf.basedb.core.DerivedBioAssay
public class DerivedBioAssay
Nested Class Summary | |
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(package private) static class |
DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
Whenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes. |
Field Summary | |
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static String |
ARRANGEMENT
The id for the DerivedBioAssayType item representing
sequenced data that has been aligned to a reference database. |
private boolean |
extractHasBeenSet
|
private boolean |
hardwareHasBeenSet
|
private boolean |
protocolHasBeenSet
|
static String |
SCAN
The id for the DerivedBioAssayType item representing a
scanned hybridization. |
static String |
SEQUENCES
The id for the DerivedBioAssayType item representing
original sequenced data. |
private boolean |
softwareHasBeenSet
|
static Item |
TYPE
The type of item represented by this class. |
Fields inherited from interface net.sf.basedb.core.Nameable |
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MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH |
Constructor Summary | |
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DerivedBioAssay(DerivedBioAssayData data)
|
Method Summary | |
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void |
addParent(DerivedBioAssay bioAssay)
Add a derived bioassay as a parent to this derived bioassay. |
void |
addPhysicalBioAssay(PhysicalBioAssay bioAssay)
Add a physical bioassay as a parent to this derived bioassay. |
long |
countRawBioAssays()
Counts all raw bioassays that have been created from this bioassay. |
Set<Annotatable> |
getAnnotatableParents()
Get the extract and parent bioassays or physical bioassays. |
ArrayDesign |
getArrayDesign()
Get the array design connected to this derived bioassay by following the path from the physical bioassay to the array slide to the array batch to the array design. |
static DerivedBioAssay |
getById(DbControl dc,
int id)
Get a DerivedBioAssay item when you know the id. |
ItemQuery<DerivedBioAssay> |
getChildren()
Get all child derived bioassays. |
Date |
getEntryDate()
Get the date that the item was registered in the database. |
Extract |
getExtract()
Get the extract that is the parent of the data in this derived bioassay. |
FileSet |
getFileSet()
Get the file set that collects all files that holds data for this item. |
Hardware |
getHardware()
Get the Hardware that was used when
creating this bioassay set. |
ItemSubtype |
getItemSubtype()
Get the subtype of the item. |
Job |
getJob()
Get the job that created this bioassay. |
static DerivedBioAssay |
getNew(DbControl dc,
boolean isRoot,
Job job)
Create a new parent-less derived bioassay. |
static DerivedBioAssay |
getNew(DbControl dc,
DerivedBioAssay parent,
Job job)
Create a new child derived bioassay from a parent derived bioassay. |
static DerivedBioAssay |
getNew(DbControl dc,
PhysicalBioAssay bioAssay,
Job job)
Create a new (root) derived bioassay from a physical bioassay. |
DerivedBioAssay |
getParent()
Deprecated. In 3.2, replaced with getParents() |
Collection<FileSet> |
getParentFileSets()
Get the file sets of parent item(s) that are related to the current item. |
ItemQuery<DerivedBioAssay> |
getParents()
Get all parent derived bioassays. |
PhysicalBioAssay |
getPhysicalBioAssay()
Deprecated. In 3.2, replaced with getPhysicalBioAssays() . |
ItemQuery<PhysicalBioAssay> |
getPhysicalBioAssays()
Get a query that returns the physical bioassays used to create this derived bioassay. |
Platform |
getPlatform()
Get the platform the item is related to. |
Protocol |
getProtocol()
Default implementation returns null. |
static ItemQuery<DerivedBioAssay> |
getQuery()
Get a query that returns derived bioassay. |
ItemQuery<RawBioAssay> |
getRawBioAssays()
|
Software |
getSoftware()
Get the Software that was used when
creating this bioassay set. |
Item |
getType()
Get the type of item represented by the object. |
Set<ItemProxy> |
getUsingItems()
Get all: Child derived bioassays Child raw bioassays |
PlatformVariant |
getVariant()
Get the platform variant the item is related to. |
boolean |
hasFileSet()
Check if this item has a file set. |
boolean |
isRoot()
Check if this bioassay set is derived from one or more physical bioassays or from derived bioassays. |
boolean |
isUsed()
Check if this item is used by some other item. |
(package private) void |
onBeforeCommit(Transactional.Action action)
Automatically try to assign an extract from parent items at creation time. |
void |
removeParent(DerivedBioAssay bioAssay)
Remove a derived bioassay as a parent item for this derived bioassay. |
void |
removePhysicalBioAssay(PhysicalBioAssay bioAssay)
Remove a physical bioassay as a parent item for this derived bioassay. |
void |
setExtract(Extract extract)
Set the extract that is the parent of data in this bioassay. |
void |
setHardware(Hardware hardware)
Set the Hardware that was used when
creating this bioassay set. |
void |
setItemSubtype(ItemSubtype subtype)
Set the subtype on the item. |
(package private) void |
setProjectDefaults(Project activeProject)
Set protocol, hardware and software from project default settings. |
void |
setProtocol(Protocol protocol)
Set the Protocol that describes the procedure used when
creating this bioassay set. |
void |
setSoftware(Software software)
Set the Software that was used when
creating this bioassay set. |
void |
testFixChildren()
|
Methods inherited from class net.sf.basedb.core.AnnotatedItem |
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getAnnotationSet, isAnnotated, removeAnnotations, toTransferable |
Methods inherited from class net.sf.basedb.core.CommonItem |
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getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable |
Methods inherited from class net.sf.basedb.core.SharedItem |
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getItemKey, getProjectKey, initPermissions, isShared, setItemKey, setProjectKey, toTransferable |
Methods inherited from class net.sf.basedb.core.OwnedItem |
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getOwner, isOwner, setOwner, takeOwnership, toTransferable |
Methods inherited from class net.sf.basedb.core.BasicItem |
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addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, toString, toTransferable, validate |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.Identifiable |
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getId, getVersion |
Methods inherited from interface net.sf.basedb.core.AccessControlled |
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checkPermission, getPermissions, hasPermission |
Methods inherited from interface net.sf.basedb.core.Ownable |
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getOwner, isOwner, setOwner, takeOwnership |
Field Detail |
---|
public static final Item TYPE
Item.DERIVEDBIOASSAY
,
getType()
public static final String SCAN
DerivedBioAssayType
item representing a
scanned hybridization.
public static final String SEQUENCES
DerivedBioAssayType
item representing
original sequenced data.
public static final String ARRANGEMENT
DerivedBioAssayType
item representing
sequenced data that has been aligned to a reference database.
private boolean extractHasBeenSet
private boolean protocolHasBeenSet
private boolean hardwareHasBeenSet
private boolean softwareHasBeenSet
Constructor Detail |
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DerivedBioAssay(DerivedBioAssayData data)
Method Detail |
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public static DerivedBioAssay getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
DerivedBioAssay
item when you know the id.
dc
- The DbControl
which will be used for
permission checking and database access.id
- The id of the item to load
DerivedBioAssay
item
ItemNotFoundException
- If an item with the specified
id is not found
PermissionDeniedException
- If the logged in user doesn't
have read permission to the item
BaseException
- If there is another errorpublic static DerivedBioAssay getNew(DbControl dc, boolean isRoot, Job job)
addPhysicalBioAssay(PhysicalBioAssay)
or
addParent(DerivedBioAssay)
.
dc
- The DbControl
which will be used for
permission checking and database accessisRoot
- TRUE if the new item is a root derived bioassay
(eg. it have physical bioassays as parent items)job
- The job that created the new bioassay
public static DerivedBioAssay getNew(DbControl dc, PhysicalBioAssay bioAssay, Job job)
dc
- The DbControl
which will be used for
permission checking and database accessbioAssay
- The parent physical bioassayjob
- The job that created the new bioassay
public static DerivedBioAssay getNew(DbControl dc, DerivedBioAssay parent, Job job)
dc
- The DbControl
which will be used for
permission checking and database accessparent
- The parent bioassayjob
- The job that created the new bioassay
public static ItemQuery<DerivedBioAssay> getQuery()
ItemQuery
objectpublic Item getType()
Identifiable
Item
enumeration.
getType
in interface Identifiable
public Set<ItemProxy> getUsingItems()
getUsingItems
in class BasicItem<DerivedBioAssayData>
BasicItem.addUsingItems(Set, Item, org.hibernate.Query)
public boolean isUsed() throws BaseException
BasicItem
super.isUsed()
, unless it has decided
that the item is used by some other means.
isUsed
in class BasicItem<DerivedBioAssayData>
BaseException
- If not able to tell if item is used or not.BasicItem.getUsingItems()
void onBeforeCommit(Transactional.Action action)
onBeforeCommit
in class SharedItem<DerivedBioAssayData>
Transactional
,
Developer documentation: Transactions,
Developer documentation: Coding rules and guidelines for item classesvoid setProjectDefaults(Project activeProject) throws BaseException
setProjectDefaults
in class BasicItem<DerivedBioAssayData>
activeProject
- The currently active project
BaseException
public Set<Annotatable> getAnnotatableParents() throws BaseException
getAnnotatableParents
in interface Annotatable
BaseException
- If there is an errorpublic Protocol getProtocol()
AnnotatedItem
getProtocol
in interface Annotatable
getProtocol
in class AnnotatedItem<DerivedBioAssayData>
@SubtypableRelatedItems(value={PHYSICALBIOASSAY,DERIVEDBIOASSAY,EXTRACT,SOFTWARE,HARDWARE,PROTOCOL}) public ItemSubtype getItemSubtype()
Subtypable
getItemSubtype
in interface Subtypable
SubtypableRelatedItems
public void setItemSubtype(ItemSubtype subtype)
Subtypable
setItemSubtype
in interface Subtypable
subtype
- A subtype or nullItemSubtype.setOnItem(Subtypable)
public Date getEntryDate()
Registered
getEntryDate
in interface Registered
public FileSet getFileSet()
FileStoreEnabled
DbControl.commit()
is called. To check if an item has files without creating a new
file set use the FileStoreEnabled.hasFileSet()
method.
getFileSet
in interface FileStoreEnabled
public boolean hasFileSet()
FileStoreEnabled
FileStoreEnabled.getFileSet()
to avoid creating a new file set when there is
no need for it.
hasFileSet
in interface FileStoreEnabled
public Platform getPlatform()
FileStoreEnabled
DataFileType
:s that can be added to the file set.
getPlatform
in interface FileStoreEnabled
public PlatformVariant getVariant()
FileStoreEnabled
DataFileType
:s that can be added to the file set.
getVariant
in interface FileStoreEnabled
public Collection<FileSet> getParentFileSets()
FileStoreEnabled
getParentFileSets
in interface FileStoreEnabled
FileSet
or null@Deprecated public PhysicalBioAssay getPhysicalBioAssay()
getPhysicalBioAssays()
.
public void testFixChildren()
public void addPhysicalBioAssay(PhysicalBioAssay bioAssay) throws PermissionDeniedException, InvalidDataException
bioAssay
- The parent bioassay to add
PermissionDeniedException
InvalidDataException
public void removePhysicalBioAssay(PhysicalBioAssay bioAssay) throws PermissionDeniedException, InvalidDataException
bioAssay
- The parent bioassay to remove from this bioassay
PermissionDeniedException
InvalidDataException
public ItemQuery<PhysicalBioAssay> getPhysicalBioAssays()
ItemQuery
object@Deprecated public DerivedBioAssay getParent()
getParents()
public void addParent(DerivedBioAssay bioAssay) throws PermissionDeniedException, InvalidDataException
bioAssay
- The parent bioassay to add
PermissionDeniedException
InvalidDataException
public void removeParent(DerivedBioAssay bioAssay) throws PermissionDeniedException, InvalidDataException
bioAssay
- The parent bioassay to remove from this bioassay
PermissionDeniedException
InvalidDataException
public ItemQuery<DerivedBioAssay> getParents()
public boolean isRoot()
public Extract getExtract()
public void setExtract(Extract extract)
extract
- The extract or nullpublic ItemQuery<DerivedBioAssay> getChildren()
public Job getJob()
public void setProtocol(Protocol protocol) throws PermissionDeniedException
Protocol
that describes the procedure used when
creating this bioassay set.
protocol
- A Protocol
item, or null if not known
PermissionDeniedException
- If the logged in user doesn't have
write permission on this event or use permission for the protocolpublic Hardware getHardware()
Hardware
that was used when
creating this bioassay set.
Hardware
item, or null if not knownpublic void setHardware(Hardware hardware) throws PermissionDeniedException
Hardware
that was used when
creating this bioassay set.
hardware
- A Hardware
item, or null if not known
PermissionDeniedException
- If the logged in user doesn't have
write permission on this event or use permission for the hardwarepublic Software getSoftware()
Software
that was used when
creating this bioassay set.
Software
item, or null if not knownpublic void setSoftware(Software software) throws PermissionDeniedException
Software
that was used when
creating this bioassay set.
software
- A Software
item, or null if not known
PermissionDeniedException
- If the logged in user doesn't have
write permission on this event or use permission for the softwarepublic ItemQuery<RawBioAssay> getRawBioAssays()
public ArrayDesign getArrayDesign() throws PermissionDeniedException, BaseException
PermissionDeniedException
- If the logged in user doesn't have
read permission for the array design
BaseException
- If there is another error.public long countRawBioAssays() throws BaseException
BaseException
- If the raw bioassays couldn't be counted.
|
3.2.1: 2012-12-13 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |