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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>
net.sf.basedb.core.MeasuredBioMaterial<ExtractData>
net.sf.basedb.core.Extract
public class Extract
This class is used to represent extract items. An extract is
created from a Sample
or by combining other extracts
(pooling). It is also possible to create
standalone extracts, with no reference to a sample or to other
extracts.
Field Summary | |
---|---|
static String |
LABELED
The id for the ExtractType item representing a
labeled extract. |
static String |
LIBRARY
The id for the ExtractType item representing a library. |
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 |
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MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH |
Constructor Summary | |
---|---|
Extract(ExtractData extractData)
|
Method Summary | |
---|---|
long |
countChildren(boolean extractsOnly)
Count the number of child extracts. |
long |
countExtracts()
Counts all extracts that have been created from this extract. |
static Extract |
getById(DbControl dc,
int id)
Get an Extract item when you know the id. |
ItemQuery<Extract> |
getChildExtracts()
Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources. |
ItemSubtype |
getItemSubtype()
Get the subtype of the item. |
static Extract |
getNew(DbControl dc)
Create a new Extract item. |
static Extract |
getNew(DbControl dc,
BioPlateEventParticipant master)
Create a new Extract item as part
of a master bioplate event. |
ItemQuery<PhysicalBioAssay> |
getPhysicalBioAssays()
Get a query that returns all bioassays created from this extract. |
static ItemQuery<Extract> |
getQuery()
Get a query that returns extracts. |
Tag |
getTag()
Get the tag that has been applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay. |
Item |
getType()
Get the type of item represented by the object. |
Set<ItemProxy> |
getUsingItems()
Get all: Child extracts created from the extract PhysicalBioAssay :s created from this extract
DerivedBioAssay :s referencing the extract
RawBioAssay :s referencing the extract
|
boolean |
isUsed()
Check that: no PhysicalBioAssay :s has been created from this item
no Extract :s has been created from this item
no DerivedBioAssay is referencing this item
no RawBioAssay is referencing this item
|
void |
setTag(Tag tag)
Set the tag that was applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay. |
Methods inherited from class net.sf.basedb.core.MeasuredBioMaterial |
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getAnnotatableParents, getBioWell, getCreationEvent, getEntryDate, getEvents, getOriginalQuantity, getParent, getParentType, getProtocol, getRemainingQuantity, hasSingleParent, isInWell, isLockedInWell, newEvent, newEvent, onBeforeCommit, setBioPlateEventParticipant, setBioWell, setOriginalQuantity, updateRemainingQuantity |
Methods inherited from class net.sf.basedb.core.BioMaterial |
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getChildCreationEvents, getExternalId, setExternalId, setItemSubtype |
Methods inherited from class net.sf.basedb.core.AnnotatedItem |
---|
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 |
---|
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, 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, 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 |
---|
public static final Item TYPE
Item.EXTRACT
,
getType()
public static final String LABELED
ExtractType
item representing a
labeled extract.
public static final String LIBRARY
ExtractType
item representing a library.
Constructor Detail |
---|
Extract(ExtractData extractData)
Method Detail |
---|
public static Extract getNew(DbControl dc) throws BaseException
Extract
item.
dc
- The DbControl
which will be used for
permission checking and database access
Extract
item
BaseException
- If there is an errorpublic static Extract getNew(DbControl dc, BioPlateEventParticipant master) throws BaseException
Extract
item as part
of a master bioplate event.
dc
- The DbControl
which will be used for
permission checking and database accessmaster
- The master bioplate event participant or null
Extract
item
BaseException
- If there is an errorpublic static Extract getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
Extract
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
Extract
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<Extract> getQuery()
ItemQuery
object.public Item getType()
Identifiable
Item
enumeration.
@SupportsPushAnnotations @SubtypableRelatedItems(value={PROTOCOL,HARDWARE,TAG,SAMPLE,EXTRACT}) public ItemSubtype getItemSubtype()
Subtypable
getItemSubtype
in interface Subtypable
getItemSubtype
in class MeasuredBioMaterial<ExtractData>
SubtypableRelatedItems
public boolean isUsed() throws BaseException
PhysicalBioAssay
:s has been created from this item
Extract
:s has been created from this item
DerivedBioAssay
is referencing this item
RawBioAssay
is referencing this item
isUsed
in class MeasuredBioMaterial<ExtractData>
BaseException
- If not able to tell if item is used or not.BasicItem.getUsingItems()
public Set<ItemProxy> getUsingItems()
PhysicalBioAssay
:s created from this extract
DerivedBioAssay
:s referencing the extract
RawBioAssay
:s referencing the extract
getUsingItems
in class MeasuredBioMaterial<ExtractData>
BasicItem.addUsingItems(Set, Item, org.hibernate.Query)
public Tag getTag()
public void setTag(Tag tag)
tag
- The tag, or null if the extract is not taggedpublic ItemQuery<Extract> getChildExtracts()
public long countExtracts() throws BaseException
BaseException
- If there is some kind of error.public long countChildren(boolean extractsOnly)
countChildren
in class BioMaterial<ExtractData>
extractsOnly
- If TRUE, the count is for biomaterials of the same type,
if FALSE the count is for biomaterials of the child typepublic ItemQuery<PhysicalBioAssay> getPhysicalBioAssays()
ItemQuery
object
|
3.2.1: 2012-12-13 | ||||||||
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