AbstractScoresCache

java.lang.Object
- org.biojava.nbio.structure.align.multiple.AbstractScoresCache

All Implemented Interfaces:

ScoresCache

Direct Known Subclasses:

BlockImpl, BlockSetImpl, MultipleAlignmentEnsembleImpl, MultipleAlignmentImpl
```
public abstract class AbstractScoresCache
extends java.lang.Object
implements ScoresCache
```
Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache.

Since:

4.1.0

Author:

Spencer Bliven

Constructor Summary

Constructors
Modifier Constructor Description

protected AbstractScoresCache()

protected AbstractScoresCache(AbstractScoresCache cache)

Constructors
Modifier	Constructor	Description
`protected`	`AbstractScoresCache()`
`protected`	`AbstractScoresCache(AbstractScoresCache cache)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`clear()`	Clear the cached scores.
`protected java.lang.Object`	`clone(java.lang.Object e)`	Subclasses should override clone and use the copy constructor.
`java.lang.Double`	`getScore(java.lang.String property)`	Get the value for a particular score.
`java.util.Set<java.lang.String>`	`getScores()`	Get a collection of all scores that have been set.
`void`	`putScore(java.lang.String property, java.lang.Double score)`	Add a score to the list of scores.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AbstractScoresCache
```
protected AbstractScoresCache()
```
  - AbstractScoresCache
```
protected AbstractScoresCache(AbstractScoresCache cache)
```
- Method Detail
  - putScore
```
public void putScore(java.lang.String property,
                     java.lang.Double score)
```
    Description copied from interface: ScoresCache
    
    Add a score to the list of scores.
    
    Specified by:
    
    putScore in interface ScoresCache
    
    Parameters:
    
    property - A string identifying the score and suitable for printing in headers. Example names found in: MultipleAlignmentScorer.
    
    score - Value of the score
  - getScore
```
public java.lang.Double getScore(java.lang.String property)
```
    Description copied from interface: ScoresCache
    
    Get the value for a particular score. Scores which return null should be recalculated and then stored using ScoresCache.putScore(String, Double).
    
    Specified by:
    
    getScore in interface ScoresCache
    
    Parameters:
    
    property - Name of the score to fetch
    
    Returns:
    
    Value of the score, or null if it is not set.
  - getScores
```
public java.util.Set<java.lang.String> getScores()
```
    Description copied from interface: ScoresCache
    
    Get a collection of all scores that have been set.
    
    Specified by:
    
    getScores in interface ScoresCache
    
    Returns:
    
    Set of all score names
  - clone
```
protected java.lang.Object clone(java.lang.Object e)
                          throws java.lang.CloneNotSupportedException
```
    Subclasses should override clone and use the copy constructor.
    
    Parameters:
    
    e -
    
    Returns:
    
    Throws:
    
    java.lang.CloneNotSupportedException
  - clear
```
public void clear()
```
    Clear the cached scores. This frees memory after the alignment changed.

Class AbstractScoresCache

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AbstractScoresCache

AbstractScoresCache

Method Detail

putScore

getScore

getScores

clone

clear