Package org.biojava.bio.dp

Class WeightMatrixAnnotator

java.lang.Object

org.biojava.bio.dp.WeightMatrixAnnotator

All Implemented Interfaces:

Serializable, SequenceAnnotator

public class WeightMatrixAnnotator
extends Object
implements SequenceAnnotator, 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, Tanya Vavouri

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
WeightMatrixAnnotator(WeightMatrix wm, double threshold)	Create a new annotator that uses PROBABILITY score type.
WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold)	Create a new annotator that uses a specific score type.
WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold, String wmID)	Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix.

Method Summary

Modifier and Type	Method	Description
Sequence	annotate(Sequence seq)	Return an annotated version of a sequence.
String	getWeightMatrixID()	Get the value of the weight matrix id.
void	setWeightMatrixID(String id)	Set the weight matrix id.

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,
                             ScoreType scoreType,
                             double threshold,
                             String wmID)

Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix.

Parameters:

wm - the weight matrix

threshold - the threshold

wmID - the weight matrix ID

WeightMatrixAnnotator

public WeightMatrixAnnotator(WeightMatrix wm,
                             double threshold)

Create a new annotator that uses PROBABILITY score type.

Parameters:

wm - a WeightMatrix value

threshold - a double value

WeightMatrixAnnotator

public WeightMatrixAnnotator(WeightMatrix wm,
                             ScoreType scoreType,
                             double threshold)

Create a new annotator that uses a specific score type.

Parameters:

wm - the weigth matrix

scoreType - the score type

threshold - the threshold

Since:

1.4

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

BioException - if the sequence fails to be annotated

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

getWeightMatrixID

public String getWeightMatrixID()

Get the value of the weight matrix id.

Returns:

value of the weight matrix id.

setWeightMatrixID

public void setWeightMatrixID(String id)

Set the weight matrix id.

Parameters:

id - Value to assign to the weight matrix id.