org.biojava.bio.seq

Interface SequenceAnnotator

All Known Implementing Classes:

RestrictionMapper, WeightMatrixAnnotator

public interface SequenceAnnotator

An object which adds some additional information to a Sequence.

There are two approaches which can be taken to adding features to a sequence:

1. Directly adding features to a Sequence which implements MutableFeatureHolder
2. Creating a new Sequence object which acts as a view on an underlying Sequence, and presents extra features.

At present, this interface supports both these mechanisms. It is the responsibility of the implementor to document which approach is taken.

Author:

Thomas Down

Method Summary

Methods

Modifier and Type	Method and Description
Sequence	annotate(Sequence seq) Return an annotated version of a sequence.

Method Detail

annotate

Sequence annotate(Sequence seq)
                  throws BioException,
                         IllegalAlphabetException,
                         ChangeVetoException

Return an annotated version of a sequence.

Parameters:

seq - The sequence to be annotated.

Returns:

An annotated version of seq (may be the same object).

Throws:

IllegalAlphabetException - If the sequence is over an inappropriate alphabet for the annotated method being encapsulated

BioException - if the sequence fails to be annotated

ChangeVetoException - if either the sequence doesn't allow annotation or if the change was vetoed