org.proteios.core

Class Extract

java.lang.Object

org.proteios.core.BasicItem<D>

org.proteios.core.OwnedItem<D>

org.proteios.core.SharedItem<D>

org.proteios.core.CommonItem<D>

org.proteios.core.AnnotatedItem<D>

org.proteios.core.BioMaterial<D>

org.proteios.core.MeasuredBioMaterial<ExtractData>

org.proteios.core.Extract

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, 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: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

Fields

Modifier and Type	Field and Description
static Item	TYPE The type of item represented by this class.

Fields inherited from class org.proteios.core.BioMaterial

MAX_EXTERNAL_ID_LENGTH, MAX_STORAGE_LOCATION_LENGTH

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

Methods

Modifier and Type	Method and Description
Set<Annotatable>	getAnnotatableParents() Get the sample or pooled extracts.
ItemQuery<LabeledExtract>	getLabeledExtracts() Get a query that returns all labeled extracts created from this extract.
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.
boolean	isUsed() Check that: no LabeledExtract:s has been created from this item no Extract:s has been created from this item
void	setSample(Sample sample) Set the Sample item that is the the parent of this extract.

Methods inherited from class org.proteios.core.MeasuredBioMaterial

getConcentrationInGramsPerLiter, getCreationEvent, getEventQuery, getEvents, getOriginalQuantityInMicroLiters, getRemainingQuantityInMicroLiters, isPooled, setConcentrationInGramsPerLiter, setCreationEvent, setOriginalQuantityInMicroLiters, setPooled, setRemainingQuantityInMicroLiters

Methods inherited from class org.proteios.core.BioMaterial

addFile, getExternalId, getFiles, getStorageLocation, removeFile, setExternalId, setFiles, setStorageLocation

Methods inherited from class org.proteios.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class org.proteios.core.SharedItem

getItemKey, getProjectKey, isShared, setItemKey, setProjectKey

Methods inherited from class org.proteios.core.OwnedItem

getOwner, setOwner

Methods inherited from class org.proteios.core.BasicItem

checkPermission, equals, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.proteios.core.Identifiable

getId, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.EXTRACT, getType()

Method Detail

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.

Throws:

BaseException

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

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)
               throws PermissionDeniedException,
                      InvalidDataException,
                      BaseException

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

Parameters:

sample - The new Sample item 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

getLabeledExtracts

public ItemQuery<LabeledExtract> getLabeledExtracts()

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

Returns:

An ItemQuery object