Package 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 Details

    • AbstractScoresCache

      protected AbstractScoresCache()

    • AbstractScoresCache

      protected AbstractScoresCache(AbstractScoresCache cache)

  • Method Details

    • 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.