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

Method Detail

addAnnotation

void addAnnotation(BiologicalAnnotation a)

Adds an annotation to the list.

removeAnnotation

boolean removeAnnotation(BiologicalAnnotation a)

Removes an annotation from this list.

Parameters:

a - the annotation to be removed.

Returns:

true if the argument was part of these annotations; false otherwise.

getAnnotations

BiologicalAnnotation[] getAnnotations()

Returns the annotations in a array.

getResidueURL

URL getResidueURL(int position)

Returns the URL anchored to the index position.

findAnnotation

Object findAnnotation(Class annotation_class)

Finds the annotation that supports the interface annotation_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