org.biojava.bio.seq
Interface SequenceAnnotator
- All Known Implementing Classes:
- 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:
- Directly adding features to a Sequence which implements
MutableFeatureHolder
- 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
annotate
public Sequence annotate(Sequence seq)
throws BioException,
IllegalAlphabetException
- Return an annotated version of a sequence.
- Parameters:
seq
- The sequence to be annotated.- Throws:
- IllegalAlphabetException - If the sequence is over
an inappropriate alphabet for
the annotated method being
encapsulated.
- BioException - if the sequence cannot be annotated.