net.sf.basedb.core
Interface Annotatable

All Superinterfaces:

AccessControlled, Identifiable

All Known Subinterfaces:

AnnotatableProxy

All Known Implementing Classes:

AnnotatedItem, ArrayBatch, ArrayDesign, ArraySlide, BioAssay, BioAssaySet, BioMaterial, BioPlate, BioSource, Extract, Hybridization, LabeledExtract, MeasuredBioMaterial, Plate, PluginConfiguration, PluginDefinition, Protocol, RawBioAssay, Sample, Scan, Well

public interface Annotatable
extends Identifiable

This interface is implemented by all items which can be annotated. Annotations are extra values attached to an item. Usually these values are used in the analysis of an experiment.

Version:

2.0

Author:

Nicklas

See Also:

AnnotationSet, Annotation, AnnotationType

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Method Summary

Set<Annotatable>	getAnnotatableParents() Get all parents objects which are annotatable and the logged in user has read permission to.
AnnotationSet	getAnnotationSet() Get the annotation set containing the annotations for this item.
Protocol	getProtocol() A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.
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 interface net.sf.basedb.core.Identifiable

getId, getType, getVersion

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

checkPermission, getPermissions, hasPermission

Method Detail

getAnnotationSet

AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
                                      BaseException

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 isAnnotated() method.

Returns:

An AnnotationSet

Throws:

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

BaseException - If there is another error

isAnnotated

boolean isAnnotated()

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

Returns:

TRUE if an annotation set exists, FALSE otherwise

removeAnnotations

void removeAnnotations()
                       throws PermissionDeniedException,
                              BaseException

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

Throws:

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

BaseException - If there is another error

getAnnotatableParents

Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get all parents objects which are annotatable and the logged in user has read permission to. If the item doesn't have any annotatable parents, it may return null or an empty set. The method should only return the immediate parent(s), not parents to parents, etc.

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getProtocol

Protocol getProtocol()

A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.

Returns:

A protocol or null if the protocol is unknown

Since:

2.2