org.proteios.core
Class Sample

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<SampleData>
                              org.proteios.core.Sample

All Implemented Interfaces:

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

public class Sample
extends MeasuredBioMaterial<SampleData>

This class is used to represent sample items. A sample is the actual sample taken from a BioSource. A sample can also be created by combining other samples into a new sample. A process is known as pooling. It is also possible to create standalone samples, with no reference to a biosource or to other samples.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

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

Set<Annotatable>	getAnnotatableParents() Get the biosource or pooled samples.
BioSource	getBioSource() Get the BioSource that is the parent of this sample.
static Sample	getById(DbControl dc, int id) Get an Sample item when you know the id.
ItemQuery<Extract>	getExtracts() Get a query that returns all extracts created from this sample.
static ItemQuery<Sample>	getQuery() Get a query that returns samples.
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no Extract:s has been created from this item no Sample:s has been created from this item
void	setBioSource(BioSource bioSource) Set the BioSource item that is the the parent of this sample.

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, 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.SAMPLE, getType()

Method Detail

getById

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

Get an Sample 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 Sample 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<Sample> getQuery()

Get a query that returns samples.

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 biosource or pooled samples.

Throws:

BaseException

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no Extract:s has been created from this item
• no Sample:s has been created from this item

Overrides:

isUsed in class MeasuredBioMaterial<SampleData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getBioSource

public BioSource getBioSource()
                       throws PermissionDeniedException,
                              BaseException

Get the BioSource that is the parent of this sample.

Returns:

A BioSource object or null if this is a pooled or standalone sample

Throws:

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

BaseException - If there is another error

setBioSource

public void setBioSource(BioSource bioSource)
                  throws PermissionDeniedException,
                         InvalidDataException

Set the BioSource item that is the the parent of this sample.

Parameters:

bioSource - The parent BioSource item

Throws:

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

InvalidDataException - If this is a pooled sample

BaseException - If there is another error

getExtracts

public ItemQuery<Extract> getExtracts()
                               throws BaseException

Get a query that returns all extracts created from this sample.

Returns:

An ItemQuery object

Throws:

BaseException