org.biojava3.alignment.template
Class AbstractScorer

java.lang.Object
  extended by org.biojava3.alignment.template.AbstractScorer
All Implemented Interfaces:
Scorer
Direct Known Subclasses:
AbstractMatrixAligner, FractionalIdentityScorer, FractionalSimilarityScorer, StandardRescoreRefiner

public abstract class AbstractScorer
extends Object
implements Scorer

Implements common code for algorithms which compute a score.

Author:
Mark Chapman

Constructor Summary
AbstractScorer()
           
 
Method Summary
 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.biojava3.alignment.template.Scorer
getMaxScore, getMinScore, getScore
 

Constructor Detail

AbstractScorer

public AbstractScorer()
Method Detail

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