Package 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, DerivedBioAssay, Experiment, Extract, File, FileServer, Hardware, ItemList, Kit, MeasuredBioMaterial, PhysicalBioAssay, Plate, PluginConfiguration, PluginDefinition, Project, Protocol, RawBioAssay, RootRawBioAssay, Sample, Software, Tag, 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: 2012-02-23 15:45:07 +0100 (to, 23 feb 2012) $

  • Method Details

    • 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. As of BASE 3.1 this method may also return child items if the child item is a Subtypable item that has a subtype with the ItemSubtype.getPushAnnotations() flag set.
      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