Package net.sf.basedb.core

Class AnnotatedItem

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.OwnedItem

net.sf.basedb.core.SharedItem

net.sf.basedb.core.CommonItem

net.sf.basedb.core.AnnotatedItem

All Implemented Interfaces:

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

Direct Known Subclasses:

ArrayBatch, ArrayDesign, ArraySlide, BioMaterial, BioPlate, DerivedBioAssay, Experiment, File, FileServer, Hardware, ItemList, Kit, PhysicalBioAssay, Plate, PluginConfiguration, Protocol, RawBioAssay, Software, Tag

public abstract class AnnotatedItem
extends CommonItem
implements Annotatable

This is a helper class for items that need to implement the Annotatable interface. Most of those items should be able to extend this class.

Version:

2.0

Author:

Nicklas

See Also:

Annotatable

Last modified

$Date: 2016-04-20 08:42:14 +0200 (on, 20 apr 2016) $

Field Summary

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Constructors

Constructor	Description
AnnotatedItem(AnnotatedData annotatedData)

Method Summary

Modifier and Type	Method	Description
AnnotationSet	getAnnotationSet()	Get the annotation set containing the annotations for this item.
(package private) AnnotatedData	getData()	Get the BasicData object that holds all data for this item.
Protocol	getProtocol()	Default implementation returns null.
boolean	isAnnotated()	Check if this item has an annotation set.
void	removeAnnotations()	Remove all annotations from this item, by deleting the annotation set.

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

getDescription, getName, getRemovedBy, isRemoved, setDescription, setName, setRemoved

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

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey

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

getOwner, isOwner, setOwner, takeOwnership

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, toString, validate

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Annotatable

getAnnotatableParents

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getType, getVersion

Methods inherited from interface net.sf.basedb.core.Ownable

getOwner, isOwner, setOwner, takeOwnership

Constructor Details

AnnotatedItem

AnnotatedItem(AnnotatedData annotatedData)

Method Details

getData

AnnotatedData getData()

Description copied from class: BasicItem

Get the BasicData object that holds all data for this item.

Overrides:

getData in class CommonItem

getAnnotationSet

public AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Get the annotation set containing the annotations for this item. If the item doesn't have any annotations a new annotation set is created and automatically saved to the database when DbControl.commit() is called. To check if an item has annotations without creating a new annotation set use the Annotatable.isAnnotated() method.

Specified by:

getAnnotationSet in interface Annotatable

Returns:

An AnnotationSet

Throws:

PermissionDeniedException - If the logged in user doesn't have enough permissions

BaseException - If there is another error

isAnnotated

public boolean isAnnotated()

Description copied from interface: Annotatable

Check if this item has an annotation set. The annotation set may be empty.

Specified by:

isAnnotated in interface Annotatable

Returns:

TRUE if an annotation set exists, FALSE otherwise

removeAnnotations

public void removeAnnotations()
                       throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Remove all annotations from this item, by deleting the annotation set.

Specified by:

removeAnnotations in interface Annotatable

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is another error

getProtocol

public Protocol getProtocol()

Default implementation returns null. Should be overriden by subclasses that has protocols.

Specified by:

getProtocol in interface Annotatable

Returns:

Always null

Since:

2.2