|
3.2.1: 2012-12-13 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
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<BioSourceData>
net.sf.basedb.core.BioSource
public class BioSource
This class represent biosource items. A biosource has
information about the source of material used in an experiment,
such as a cell line or patient. A biosource can be used to
create Sample
:s.
Field Summary | |
---|---|
static Item |
TYPE
The type of item represented by this class. |
Fields inherited from class net.sf.basedb.core.BioMaterial |
---|
MAX_EXTERNAL_ID_LENGTH |
Fields inherited from interface net.sf.basedb.core.Nameable |
---|
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH |
Constructor Summary | |
---|---|
BioSource(BioSourceData bioSourceData)
|
Method Summary | |
---|---|
long |
countChildren(boolean pooled)
Count the number of child samples. |
long |
countSamples()
Counts all samples that have been created from this biosource. |
static BioSource |
getById(DbControl dc,
int id)
Get an BioSource item when you know the id. |
Date |
getEntryDate()
Get the date that the item was registered in the database. |
static BioSource |
getNew(DbControl dc)
Create a new BioSource item. |
static ItemQuery<BioSource> |
getQuery()
Get a query that returns biosource items. |
ItemQuery<Sample> |
getSamples()
Get a query that returns all samples created from this biosource. |
Item |
getType()
Get the type of item represented by the object. |
Set<ItemProxy> |
getUsingItems()
Get all: Sample :s created from this biosource
|
boolean |
isUsed()
Check that: no Sample has been created from this biosource
|
Sample |
newSample()
Create a new Sample from this biosource. |
Methods inherited from class net.sf.basedb.core.BioMaterial |
---|
getAnnotatableParents, getChildCreationEvents, getExternalId, getItemSubtype, onBeforeCommit, setExternalId, setItemSubtype |
Methods inherited from class net.sf.basedb.core.AnnotatedItem |
---|
getAnnotationSet, getProtocol, isAnnotated, removeAnnotations, toTransferable |
Methods inherited from class net.sf.basedb.core.CommonItem |
---|
getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable |
Methods inherited from class net.sf.basedb.core.SharedItem |
---|
getItemKey, getProjectKey, initPermissions, isShared, setItemKey, setProjectKey, toTransferable |
Methods inherited from class net.sf.basedb.core.OwnedItem |
---|
getOwner, isOwner, setOwner, takeOwnership, toTransferable |
Methods inherited from class net.sf.basedb.core.BasicItem |
---|
addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, 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 |
Methods inherited from interface net.sf.basedb.core.Ownable |
---|
getOwner, isOwner, setOwner, takeOwnership |
Field Detail |
---|
public static final Item TYPE
Item.BIOSOURCE
,
getType()
Constructor Detail |
---|
BioSource(BioSourceData bioSourceData)
Method Detail |
---|
public static BioSource getNew(DbControl dc) throws BaseException
BioSource
item.
dc
- The DbControl
which will be used for
permission checking and database access
BioSource
item
BaseException
- If there is an errorpublic static BioSource getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
BioSource
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
BioSource
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 ItemQuery<BioSource> getQuery()
ItemQuery
object.public Item getType()
Identifiable
Item
enumeration.
getType
in interface Identifiable
public Date getEntryDate()
Registered
getEntryDate
in interface Registered
public boolean isUsed() throws BaseException
Sample
has been created from this biosource
isUsed
in class BasicItem<BioSourceData>
BaseException
- If not able to tell if item is used or not.BasicItem.getUsingItems()
public Set<ItemProxy> getUsingItems()
Sample
:s created from this biosource
getUsingItems
in class BasicItem<BioSourceData>
BasicItem.addUsingItems(Set, Item, org.hibernate.Query)
public Sample newSample() throws PermissionDeniedException, BaseException
Sample
from this biosource.
Sample
item
PermissionDeniedException
- If the logged in user doesn't have
use permission for this biosource
BaseException
- If there is another errorpublic ItemQuery<Sample> getSamples()
ItemQuery
objectpublic long countSamples() throws BaseException
BaseException
- If counting the samples fails.public long countChildren(boolean pooled)
countChildren
in class BioMaterial<BioSourceData>
pooled
- If TRUE, the count is for biomaterials of the same type,
if FALSE the count is for biomaterials of the child type
|
3.2.1: 2012-12-13 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |