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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<D>
net.sf.basedb.core.BioMaterial<D>
public abstract class BioMaterial<D extends BioMaterialData>
This is the base class for for the three types of biomaterials:
BioSource
, Sample
and Extract
.
Field Summary | |
---|---|
static int |
MAX_EXTERNAL_ID_LENGTH
The maximum length of the external id that can be stored in the database. |
Fields inherited from interface net.sf.basedb.core.Nameable |
---|
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH |
Constructor Summary | |
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BioMaterial(D bioMaterialData)
|
Method Summary | |
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abstract long |
countChildren(boolean pooled)
Count the number of already existing children to this biomaterial. |
Set<Annotatable> |
getAnnotatableParents()
Get all child biomaterial items with a subtype that has the ItemSubtype.getPushAnnotations() flag set. |
static BioMaterial |
getById(DbControl dc,
int id)
Get a biomaterial item when you know the id. |
SpecialQuery<BioMaterialEventSource> |
getChildCreationEvents()
Get a query returning all events where this biomaterial has been used as a source item. |
String |
getExternalId()
Get the external id of the biomaterial. |
ItemSubtype |
getItemSubtype()
Get the subtype of the item. |
(package private) void |
onBeforeCommit(Transactional.Action action)
On delete action: issue an update to decrease the size of all BioMaterialList :s this is a member of. |
void |
setExternalId(String externalId)
Set the external id of the biomaterial. |
void |
setItemSubtype(ItemSubtype subtype)
Set the subtype on the item. |
Methods inherited from class net.sf.basedb.core.AnnotatedItem |
---|
getAnnotationSet, getProtocol, 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, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, 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, getType, 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 |
---|
getOwner, isOwner, setOwner, takeOwnership |
Field Detail |
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public static final int MAX_EXTERNAL_ID_LENGTH
setExternalId(String)
,
Constant Field ValuesConstructor Detail |
---|
BioMaterial(D bioMaterialData)
Method Detail |
---|
public static BioMaterial getById(DbControl dc, int id)
BioMaterial
. Eg. BioSource
,
Sample
or Extract
.
dc
- The DbControl
which will be used for
permission checking and database access.id
- The id of the item to load
Sample
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 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 Set<Annotatable> getAnnotatableParents() throws BaseException
ItemSubtype.getPushAnnotations()
flag set.
getAnnotatableParents
in interface Annotatable
BaseException
- If there is an errorvoid onBeforeCommit(Transactional.Action action) throws NotLoggedInException, BaseException
BioMaterialList
:s this is a member of.
onBeforeCommit
in class SharedItem<D extends BioMaterialData>
NotLoggedInException
- If no user is logged in
BaseException
- If there is another errorTransactional
,
Developer documentation: Transactions,
Developer documentation: Coding rules and guidelines for item classespublic String getExternalId()
public void setExternalId(String externalId) throws PermissionDeniedException, InvalidDataException
MAX_EXTERNAL_ID_LENGTH
constant.
externalId
- The new value for the external id
PermissionDeniedException
- If the logged in user doesn't have
write permission
InvalidDataException
- If the string is too longpublic abstract long countChildren(boolean pooled)
pooled
- If TRUE, the count is for biomaterials of the same type,
if FALSE the count is for biomaterials of the child typepublic SpecialQuery<BioMaterialEventSource> getChildCreationEvents()
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