|
2.17.2: 2011-06-17 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object net.sf.basedb.core.BasicItem<D> net.sf.basedb.core.ChildItem<WellData> net.sf.basedb.core.Well
public class Well
A well is located on a Plate
and contains a ReporterData
.
If the plate the well is located on was created from some other plates
via a PlateMapping
the well also contains a reference back
to the parent well on one of the source plates.
Once the well has been saved to the database it cannot be modified, except for annotations.
Plate
Field Summary | |
---|---|
static Item |
TYPE
The type of item represented by this class. |
Constructor Summary | |
---|---|
Well(WellData wellData)
|
Method Summary | |
---|---|
Set<Annotatable> |
getAnnotatableParents()
Get the parent well, if any. |
AnnotationSet |
getAnnotationSet()
Get the annotation set containing the annotations for this item. |
static Well |
getById(DbControl dc,
int id)
Get a Well item when you know the id. |
int |
getColumn()
Get the column coordinate of this well on the plate. |
Well |
getParent()
Get the parent well. |
Plate |
getPlate()
Get the Plate this event belongs to. |
Protocol |
getProtocol()
A protcol used in the creation of an item that is used to attach annotations for the protocol parameters. |
static ItemQuery<Well> |
getQuery(Plate plate)
Get a query configured to retrieve wells for a plate. |
ReporterData |
getReporter()
Get the reporter in this well. |
ReporterData |
getReporter(boolean forceInitialization)
Get the reporter in this well. |
int |
getRow()
Get the row coordinate of this well on the plate. |
(package private) SharedData |
getSharedParent()
Get the shareable parent item of this child item. |
Item |
getType()
Get the type of item represented by the object. |
Set<ItemProxy> |
getUsingItems()
Get all: Child wells Features derived from this well |
boolean |
isAnnotated()
Check if this item has an annotation set. |
boolean |
isUsed()
Check if: a Feature is linked to this well
another Well has this well as it's parent well
|
void |
removeAnnotations()
Remove all annotations from this item, by deleting the annotation set. |
(package private) void |
setParent(Well parent)
Set the parent well. |
void |
setReporter(ReporterData reporter)
Set the reporter of this well. |
Methods inherited from class net.sf.basedb.core.ChildItem |
---|
getPermissionForWriteDeleteAndCreate, getPluginPermissions, initPermissions |
Methods inherited from class net.sf.basedb.core.BasicItem |
---|
addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate |
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.Identifiable |
---|
getId, getVersion |
Methods inherited from interface net.sf.basedb.core.AccessControlled |
---|
checkPermission, getPermissions, hasPermission |
Field Detail |
---|
public static final Item TYPE
Item.WELL
,
getType()
Constructor Detail |
---|
Well(WellData wellData)
Method Detail |
---|
public static Well getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
Well
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
Well
item
ItemNotFoundException
- If an item with the specified
id is not found
PermissionDeniedException
- If the logged in user doesn't
have Permission.READ
permission to the item
BaseException
- If there is another errorpublic static ItemQuery<Well> getQuery(Plate plate) throws InvalidDataException
plate
- The plate to retreive wells for, null is not allowed
ItemQuery
object
InvalidDataException
- If required parameter is null.Plate.getEvents()
public Item getType()
Identifiable
Item
enumeration.
getType
in interface Identifiable
public AnnotationSet getAnnotationSet() throws PermissionDeniedException, BaseException
Annotatable
DbControl.commit()
is
called. To check if an item has annotations without creating a new
annotation set use the Annotatable.isAnnotated()
method.
getAnnotationSet
in interface Annotatable
AnnotationSet
PermissionDeniedException
- If the logged in user doesn't have
enough permissions
BaseException
- If there is another errorpublic boolean isAnnotated()
Annotatable
isAnnotated
in interface Annotatable
public void removeAnnotations() throws PermissionDeniedException, BaseException
Annotatable
removeAnnotations
in interface Annotatable
PermissionDeniedException
- If the logged in user doesn't have
write permission
BaseException
- If there is another errorpublic Set<Annotatable> getAnnotatableParents() throws BaseException
getAnnotatableParents
in interface Annotatable
BaseException
- If there is an errorpublic Protocol getProtocol()
Annotatable
getProtocol
in interface Annotatable
public boolean isUsed() throws BaseException
isUsed
in class BasicItem<WellData>
BaseException
- If not able to tell if item is used or not.BasicItem.getUsingItems()
public Set<ItemProxy> getUsingItems()
getUsingItems
in class BasicItem<WellData>
BasicItem.addUsingItems(Set, Item, org.hibernate.Query)
SharedData getSharedParent()
ChildItem
ChildItem.initPermissions(int, int)
method to calculate
the logged in user's permissions for the child item.
getSharedParent
in class ChildItem<WellData>
public Plate getPlate() throws PermissionDeniedException, BaseException
Plate
this event belongs to.
Plate
item
PermissionDeniedException
- If the logged in user doesn't have
Permission.READ
permission for the plate
BaseException
- If there is another errorpublic int getRow()
public int getColumn()
public Well getParent() throws PermissionDeniedException, BaseException
PlateMapping
.
Well
item or null if this plate has no
parents
PermissionDeniedException
- If the logged in user doesn't have
read permission to the parent well
BaseException
- If there is another errorvoid setParent(Well parent)
PlateMapping
when
creating new plates from a mapping. This method also sets
the reporter to the same reporter as the parent well.
public ReporterData getReporter() throws PermissionDeniedException, BaseException
ReporterData
object or null if no
reporter has been specified
PermissionDeniedException
- If the logged in user doesn't
have read permission to reporters
BaseException
- If there is another errorpublic ReporterData getReporter(boolean forceInitialization)
forceInitialization
- TRUE if the initialization of
the reporter should be forced, FALSE otherwise.
ReporterData
object or null if no
reporter has been specified.public void setReporter(ReporterData reporter) throws PermissionDeniedException
reporter
- The new reporter or null if the reporter is unknown
PermissionDeniedException
- If this well has been saved to
the database or a parent well has been set (in which case the reporter
must always be the same as for the parent) or the logged in user
doesn't have write permission for the well or use permission
for reporters
|
2.17.2: 2011-06-17 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |