org.biojava.nbio.structure.align.multiple

Class 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 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 and Description
protected	AbstractScoresCache()
protected	AbstractScoresCache(AbstractScoresCache cache)

Method Summary

Modifier and Type	Method and Description
void	clear() Clear the cached scores.
protected Object	clone(Object e) Subclasses should override clone and use the copy constructor.
Double	getScore(String property) Get the value for a particular score.
Set<String>	getScores() Get a collection of all scores that have been set.
void	putScore(String property, 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(String property,
                     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 Double getScore(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 Set<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 Object clone(Object e)
                throws CloneNotSupportedException

Subclasses should override clone and use the copy constructor.

Parameters:

e -

Returns:

Throws:

CloneNotSupportedException

clear

public void clear()

Clear the cached scores. This frees memory after the alignment changed.