net.sf.basedb.core
Class LabeledExtract

java.lang.Object
  net.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<LabeledExtractData>
                              net.sf.basedb.core.LabeledExtract

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable

public class LabeledExtract
extends MeasuredBioMaterial<LabeledExtractData>

This class is used to represent labeled extract items. A labeled extract is an Extract that has been marked with a Label. It is also possible to create a labled extract by combining other labeled extracts, or as a standalone item with no reference to an extract or other labeled extracts.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2010-12-02 14:35:04 +0100 (Thu, 02 Dec 2010) $

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

LabeledExtract(LabeledExtractData labeledExtractData)

Method Summary

long	countChildren(boolean pooled) Count the number of child labeled extracts.
long	countLabeledExtracts() Counts all labeled extracts that have been created from this labeled extract.
Set<Annotatable>	getAnnotatableParents() Get the extract or pooled labeled extracts.
static LabeledExtract	getById(DbControl dc, int id) Get a LabeledExtract item when you know the id.
ItemQuery<LabeledExtract>	getChildLabeledExtracts() Creates a query that returns all child (pooled) labeled extracts that has this labeled extracts as one of it's sources.
Extract	getExtract() Get the Extract that is the parent of this labeled extract.
ItemQuery<Hybridization>	getHybridizations() Get a query that returns all hybridizations created from this labeled extract.
Label	getLabel() Get the Label compound used for labeling the extract.
static LabeledExtract	getNew(DbControl dc, Label label) Create a new LabeledExtract item.
static LabeledExtract	getNew(DbControl dc, Label label, BioPlateEventParticipant master) Create a new LabeledExtract item as part of a master bioplate event.
static ItemQuery<LabeledExtract>	getQuery() Get a query that returns labeled extracts.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Hybridization:s created from this labeled extract
boolean	isUsed() Check that: no Hybridization:s has been created from this item no LabeledExtract:s has been created from this item
void	setExtract(Extract extract, Float usedQuantity) Set the Extract item that is the parent of this labeled extract.
void	setLabel(Label label) Set the Label that was used to label the extract.

Methods inherited from class net.sf.basedb.core.MeasuredBioMaterial

getBioWell, getCreationEvent, getEntryDate, getEvents, getOriginalQuantity, getPoolingEvents, getProtocol, getRemainingQuantity, isInWell, isLockedInWell, isPooled, newEvent, newEvent, onBeforeCommit, setBioPlateEventParticipant, setBioWell, setOriginalQuantity, setPooled, updateRemainingQuantity

Methods inherited from class net.sf.basedb.core.BioMaterial

getExternalId, setExternalId

Methods inherited from class net.sf.basedb.core.AnnotatedItem

getAnnotationSet, 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

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.LABELEDEXTRACT, getType()

Constructor Detail

LabeledExtract

LabeledExtract(LabeledExtractData labeledExtractData)

Method Detail

getNew

public static LabeledExtract getNew(DbControl dc,
                                    Label label)
                             throws BaseException

Create a new LabeledExtract item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

label - The labeling compound used for labeling the extract

Returns:

The new LabeledExtract item

Throws:

BaseException - If there is an error

getNew

public static LabeledExtract getNew(DbControl dc,
                                    Label label,
                                    BioPlateEventParticipant master)
                             throws BaseException

Create a new LabeledExtract item as part of a master bioplate event.

Parameters:

dc - The DbControl which will be used for permission checking and database access

label - The labeling compound used for labeling the extract

master - The master bioplate event participant or null

Returns:

The new LabeledExtract item

Throws:

BaseException - If there is an error

Since:

2.17

getById

public static LabeledExtract getById(DbControl dc,
                                     int id)
                              throws ItemNotFoundException,
                                     PermissionDeniedException,
                                     BaseException

Get a LabeledExtract item when you know the id.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The id of the item to load

Returns:

The LabeledExtract item

Throws:

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 error

getQuery

public static ItemQuery<LabeledExtract> getQuery()

Get a query that returns labeled extracts.

Returns:

An ItemQuery object.

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Returns:

A value indicating the type of item

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the extract or pooled labeled extracts.

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no Hybridization:s has been created from this item
• no LabeledExtract:s has been created from this item

Overrides:

isUsed in class MeasuredBioMaterial<LabeledExtractData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException - If not able to tell if item is used or not.

See Also:

BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• Hybridization:s created from this labeled extract

  Overrides:

  getUsingItems in class MeasuredBioMaterial<LabeledExtractData>

  Returns:

  A set containing proxies for the items, or an empty set if no items are using this item

  Since:

  2.2

  See Also:

  BasicItem.addUsingItems(Set, Item, org.hibernate.Query)

getLabel

public Label getLabel()
               throws PermissionDeniedException,
                      BaseException

Get the Label compound used for labeling the extract.

Returns:

A Label object

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the label

BaseException - If there is another error

setLabel

public void setLabel(Label label)
              throws PermissionDeniedException,
                     InvalidDataException

Set the Label that was used to label the extract.

Parameters:

label - The new Label item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for this labeled extract or use permission for the label

InvalidDataException - If the label is null

BaseException - If there is another error

getExtract

public Extract getExtract()
                   throws PermissionDeniedException,
                          BaseException

Get the Extract that is the parent of this labeled extract.

Returns:

An Extract object or null if this is a pooled or standalone labeled extract

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the extract

BaseException - If there is another error

setExtract

public void setExtract(Extract extract,
                       Float usedQuantity)
                throws PermissionDeniedException,
                       InvalidDataException,
                       BaseException

Set the Extract item that is the parent of this labeled extract.

Parameters:

extract - The new Extract item

usedQuantity - Used quantity of the extract.

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for this labeled extract or use permission for the extract

InvalidDataException - If this is a pooled labeled extract

BaseException - If there is another error

getHybridizations

public ItemQuery<Hybridization> getHybridizations()

Get a query that returns all hybridizations created from this labeled extract.

Returns:

An ItemQuery object

getChildLabeledExtracts

public ItemQuery<LabeledExtract> getChildLabeledExtracts()

Creates a query that returns all child (pooled) labeled extracts that has this labeled extracts as one of it's sources.

Returns:

A query

Since:

2.10

countLabeledExtracts

public long countLabeledExtracts()
                          throws BaseException

Counts all labeled extracts that have been created from this labeled extract. The count includes labeled extracts that the logged in user doesn't have access to.

Returns:

The number of labeled extracts

Throws:

BaseException - If there is some kind of error.

Since:

2.16

countChildren

public long countChildren(boolean pooled)

Count the number of child labeled extracts. Since a labeled extract can't have non-pooled childre, this method always return 0 if pooled = false.

Specified by:

countChildren in class BioMaterial<LabeledExtractData>

Parameters:

pooled - If TRUE, the count is for biomaterials of the same type, if FALSE the count is for biomaterials of the child type

Since:

2.16