Package org.biojava.nbio.alignment.template

Class AbstractScorer

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

All Implemented Interfaces:

Scorer

Direct Known Subclasses:

AbstractMatrixAligner, FractionalIdentityScorer, FractionalSimilarityScorer, StandardRescoreRefiner, SubstitutionMatrixScorer

public abstract class AbstractScorer
extends Object
implements Scorer

Implements common code for algorithms which compute a score.

Author:

Mark Chapman

Constructor Summary

Constructors

Constructor	Description
AbstractScorer()

Method Summary

Modifier and Type	Method	Description
double	getDistance()	Returns score as a distance between 0.0 and 1.0.
double	getDistance(double scale)	Returns score as a distance between 0.0 and scale.
double	getSimilarity()	Returns score as a similarity between 0.0 and 1.0.
double	getSimilarity(double scale)	Returns score as a similarity between 0.0 and scale.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getMaxScore, getMinScore, getScore

Constructor Details

AbstractScorer

public AbstractScorer()

Method Details

getDistance

public double getDistance()

Description copied from interface: Scorer

Returns score as a distance between 0.0 and 1.0. This equals (Scorer.getMaxScore() - Scorer.getScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getDistance in interface Scorer

Returns:

score as a distance between 0.0 and 1.0

getDistance

public double getDistance(double scale)

Description copied from interface: Scorer

Returns score as a distance between 0.0 and scale. This equals scale * (Scorer.getMaxScore() - Scorer.getScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getDistance in interface Scorer

Parameters:

scale - maximum distance

Returns:

score as a distance between 0.0 and scale

getSimilarity

public double getSimilarity()

Description copied from interface: Scorer

Returns score as a similarity between 0.0 and 1.0. This equals (Scorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getSimilarity in interface Scorer

Returns:

score as a similarity between 0.0 and 1.0

getSimilarity

public double getSimilarity(double scale)

Description copied from interface: Scorer

Returns score as a similarity between 0.0 and scale. This equals scale * (Scorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getSimilarity in interface Scorer

Parameters:

scale - maximum similarity

Returns:

score as a similarity between 0.0 and scale