001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021
022package org.biojava.bio.seq.db;
023
024import java.io.IOException;
025import java.io.ObjectInputStream;
026import java.lang.ref.SoftReference;
027import java.util.HashMap;
028import java.util.Map;
029import java.util.Set;
030
031import org.biojava.bio.BioException;
032import org.biojava.bio.seq.Sequence;
033
034/**
035 * SequenceDB implementation that caches the results of another SequenceDB.
036 * 
037 * @author Matthew Pocock
038 */
039
040public class CachingSequenceDB extends SequenceDBWrapper {
041  private transient Map cache;
042  
043  /**
044   * Create a new CachingSequenceDB that caches the sequences in parent.
045   *
046   * @param parent the SequenceDB to cache
047   */
048  public CachingSequenceDB(SequenceDB parent) {
049    super(parent);
050    cache = new HashMap();
051  }
052  
053  public String getName() {
054    return getParent().getName();
055  }
056  
057  public Sequence getSequence(String id) throws BioException {
058    SoftReference ref = (SoftReference) cache.get(id);
059    Sequence seq;
060    if(ref == null) {
061      seq = getParent().getSequence(id);
062      cache.put(id, new SoftReference(seq));
063    } else {
064      seq = (Sequence) ref.get();
065      if(seq == null) {
066        seq = getParent().getSequence(id);
067        cache.put(id, new SoftReference(seq));
068      }
069    }
070    return seq;
071  }
072  
073  public Set ids() {
074    return getParent().ids();
075  }
076  
077  private void readObject(ObjectInputStream in)
078  throws IOException, ClassNotFoundException {
079    in.defaultReadObject();
080    this.cache = new HashMap();
081  }
082}