org.biojava.bio.dp
Class WeightMatrixAnnotator

java.lang.Object
  |
  +--org.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:

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

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

BioException - if the sequence fails to be annotated