RbDe rbde-349 (20120127151154)

edu.mssm.crover.representation
Interface BiologicalAnnotations

All Known Implementing Classes:
Annotations

public interface BiologicalAnnotations

Extendable annotation support for AnnotatedBioSequence objects. Stores the annotations attached to a sequence and helps find annotations in the list. According to the concept of communication between biological databases and tools you could receive information encoded in this object that is unknown to the developer of your application at the time of development. BiologicalAnnotations is designed in a way that in this case, you can obtain a default representation of the information that includes support for searching this information and for displaying it.

Author:
Fabien Campagne

Method Summary
 void addAnnotation(BiologicalAnnotation annotation)
          Adds an annotation to the list.
 Object findAnnotation(Class clazz)
          Finds the annotation that supports the interface of the specified class.
 BiologicalAnnotation[] getAnnotations()
          Returns the annotations in a array.
 URL getResidueURL(int position)
          Returns the URL anchored to the index position.
 boolean removeAnnotation(BiologicalAnnotation annotation)
          Removes an annotation from this list.
 String toString()
          Prints the content of this information.
 

Method Detail

addAnnotation

void addAnnotation(BiologicalAnnotation annotation)
Adds an annotation to the list.

Parameters:
annotation - The annotation to add

removeAnnotation

boolean removeAnnotation(BiologicalAnnotation annotation)
Removes an annotation from this list.

Parameters:
annotation - the annotation to remove
Returns:
true if the argument was part of these annotations; false otherwise.

getAnnotations

BiologicalAnnotation[] getAnnotations()
Returns the annotations in a array.

Returns:
the collection of annotations encapsulated in this object

getResidueURL

URL getResidueURL(int position)
Returns the URL anchored to the index position.

Parameters:
position - The position to get the url for
Returns:
the URL associated with the specified position

findAnnotation

Object findAnnotation(Class clazz)
Finds the annotation that supports the interface of the specified class.

Parameters:
clazz - The typs of annotation to retrieve
Returns:
The annotation that matches the specified class

toString

String toString()
Prints the content of this information. The output is a default, every bit printed, text form.

Overrides:
toString in class Object
Returns:
a string representation of the object.

RbDe rbde-349 (20120127151154)

Copyright © 2003-2012 Institute for Computational Biomedicine, All Rights Reserved.