net.sf.basedb.core
Class Extract

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<ExtractData>
                              net.sf.basedb.core.Extract

All Implemented Interfaces:

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

public class Extract
extends MeasuredBioMaterial<ExtractData>

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.

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

Extract(ExtractData extractData)

Method Summary

long	countChildren(boolean pooled) Count the number of child extracts or labeled extracts.
long	countExtracts() Counts all extracts that have been created from this extract.
long	countLabeledExtracts() Gets the number of LabeledExtract that are create from this item.
Set<Annotatable>	getAnnotatableParents() Get the sample or pooled extracts.
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.
ItemQuery<LabeledExtract>	getLabeledExtracts() Get a query that returns all labeled extracts created from this extract.
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.
static ItemQuery<Extract>	getQuery() Get a query that returns extracts.
Sample	getSample() Get the Sample that is the parent of this extract.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: LabeledExtract:s created from this extract
boolean	isUsed() Check that: no LabeledExtract:s has been created from this item no Extract:s has been created from this item
LabeledExtract	newLabeledExtract(Label label, Float usedQuantity) Create a new LabeledExtract from this extract.
LabeledExtract	newLabeledExtract(Label label, Float usedQuantity, BioPlateEventParticipant master) Create a new LabeledExtract from this extract as part of a master bioplate event.
void	setSample(Sample sample, Float usedQuantity) Set the Sample item that is the parent of this 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.EXTRACT, getType()

Constructor Detail

Extract

Extract(ExtractData extractData)

Method Detail

getNew

public static Extract getNew(DbControl dc)
                      throws BaseException

Create a new Extract item.

Parameters:

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

Returns:

The new Extract item

Throws:

BaseException - If there is an error

getNew

public static Extract getNew(DbControl dc,
                             BioPlateEventParticipant master)
                      throws BaseException

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

Parameters:

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

master - The master bioplate event participant or null

Returns:

The new Extract item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get an Extract 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 Extract 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<Extract> getQuery()

Get a query that returns 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 sample or pooled 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 LabeledExtract:s has been created from this item
• no Extract:s has been created from this item

Overrides:

isUsed in class MeasuredBioMaterial<ExtractData>

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:

• LabeledExtract:s created from this extract

  Overrides:

  getUsingItems in class MeasuredBioMaterial<ExtractData>

  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)

getSample

public Sample getSample()
                 throws PermissionDeniedException,
                        BaseException

Get the Sample that is the parent of this extract.

Returns:

A Sample object or null if this is a pooled or standalone extract

Throws:

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

BaseException - If there is another error

setSample

public void setSample(Sample sample,
                      Float usedQuantity)
               throws PermissionDeniedException,
                      InvalidDataException,
                      BaseException

Set the Sample item that is the parent of this extract.

Parameters:

sample - The new Sample item

usedQuantity - The quantity that was used from the sample when the extract was created

Throws:

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

InvalidDataException - If this is a pooled extract

BaseException - If there is another error

newLabeledExtract

public LabeledExtract newLabeledExtract(Label label,
                                        Float usedQuantity)
                                 throws PermissionDeniedException,
                                        BaseException

Create a new LabeledExtract from this extract.

Parameters:

label - The labeling compound used to label the extract

usedQuantity - The quantity used from this extract or null if not known

Returns:

The new LabeledExtract item

Throws:

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

BaseException - If there is another error

newLabeledExtract

public LabeledExtract newLabeledExtract(Label label,
                                        Float usedQuantity,
                                        BioPlateEventParticipant master)
                                 throws PermissionDeniedException,
                                        BaseException

Create a new LabeledExtract from this extract as part of a master bioplate event.

Parameters:

label - The labeling compound used to label the extract

usedQuantity - The quantity used from this extract or null if not known

master - The master bioplate event participant or null

Returns:

The new LabeledExtract item

Throws:

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

BaseException - If there is another error

Since:

2.17

getLabeledExtracts

public ItemQuery<LabeledExtract> getLabeledExtracts()

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

Returns:

An ItemQuery object

getChildExtracts

public ItemQuery<Extract> getChildExtracts()

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

Returns:

A query

Since:

2.10

countLabeledExtracts

public long countLabeledExtracts()
                          throws BaseException

Gets the number of LabeledExtract that are create from this item.

Returns:

Number of LabeledExtracts

Throws:

BaseException - If there is any error.

countExtracts

public long countExtracts()
                   throws BaseException

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

Returns:

The number of extracts

Throws:

BaseException - If there is some kind of error.

Since:

2.16

countChildren

public long countChildren(boolean pooled)

Count the number of child extracts or labeled extracts.

Specified by:

countChildren in class BioMaterial<ExtractData>

Parameters:

pooled - TRUE = count child extracts, FALSE = count child labeled extracts

Since:

2.16