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 java.lang.Object
implements Scorer
```
Implements common code for algorithms which compute a score.

Author:

Mark Chapman

Constructor Summary

Constructors
Constructor Description

AbstractScorer()

Constructors
Constructor	Description
`AbstractScorer()`

Method Summary

All Methods Instance Methods Concrete Methods
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 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

Class AbstractScorer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractScorer

Method Detail

getDistance

getDistance

getSimilarity

getSimilarity