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 java.lang.Object
implements ScoresCache

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractScoresCache()
protected	AbstractScoresCache(AbstractScoresCache cache)

Method Summary

Methods

Modifier and Type	Method and Description
void	clear() Resets all 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 which 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)

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. E.g. #SCORE_TMSCORE

score - Value of the score

persistent - Boolean indicating whether this score should be persisted across serialization, cloning, and other changes.

getScore

public java.lang.Double getScore(java.lang.String property)

Get the value for a particular score

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()

Get a collection of all scores which 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()

Resets all scores