org.biojava.bio.dp
Class WeightMatrixAnnotator

java.lang.Object
  extended byorg.biojava.bio.dp.WeightMatrixAnnotator
All Implemented Interfaces:
SequenceAnnotator, java.io.Serializable

public class WeightMatrixAnnotator
extends java.lang.Object
implements SequenceAnnotator, java.io.Serializable

Annotates a sequence with hits to a weight-matrix.

This SequenceAnnotator implementation returns a new ViewSequence wrapping the underlying Sequence

Author:
Matthew Pocock, Thomas Down
See Also:
Serialized Form

Constructor Summary
WeightMatrixAnnotator(WeightMatrix wm, double threshold)
           
 
Method Summary
 Sequence annotate(Sequence seq)
          Return an annotated version of a sequence.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

WeightMatrixAnnotator

public WeightMatrixAnnotator(WeightMatrix wm,
                             double threshold)
Method Detail

annotate

public Sequence annotate(Sequence seq)
                  throws IllegalAlphabetException,
                         BioException,
                         ChangeVetoException
Description copied from interface: SequenceAnnotator
Return an annotated version of a sequence.

Specified by:
annotate in interface SequenceAnnotator
Parameters:
seq - The sequence to be annotated.
Returns:
An annotated version of seq (may be the same object).
Throws:
ChangeVetoException - if either the sequence doesn't allow annotation or if the change was vetoed
IllegalAlphabetException - If the sequence is over an inappropriate alphabet for the annotated method being encapsulated
BioException - if the sequence fails to be annotated