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
022
023package org.biojava.bio.symbol;
024
025import java.io.InvalidObjectException;
026import java.io.ObjectStreamException;
027import java.io.Serializable;
028import java.util.List;
029
030import org.biojava.bio.Annotation;
031
032/**
033 * A basic implementation of AtomicSymbol.
034 *
035 * If you wish to construct new Symbols, you should normally do so via utility methods
036 * on <code>AlphabetManager</code>.
037 *
038 * This may be a useful base class for custom implementations.
039 *
040 * @author Matthew Pocock
041 */
042public class SimpleAtomicSymbol
043        extends AbstractSimpleBasisSymbol
044        implements AtomicSymbol, Serializable
045{
046  protected SimpleAtomicSymbol(
047    Annotation annotation, List syms
048  ) throws IllegalSymbolException {
049    super(annotation, syms);
050  }
051
052  protected Alphabet createMatches() {
053    return new SingletonAlphabet(this);
054  }
055
056  private Object writeReplace()
057  {
058    return new SBSH(this);
059  }
060
061  private static class SBSH
062          implements Serializable
063  {
064    private List syms;
065    private Annotation ann;
066
067    public SBSH(SimpleAtomicSymbol sym)
068    {
069      syms = sym.getSymbols();
070      ann = sym.getAnnotation();
071    }
072
073    public Object readResolve()
074            throws ObjectStreamException
075    {
076      try {
077        Symbol sym = AlphabetManager.createSymbol(ann, syms, null);
078        return sym;
079      } catch (IllegalSymbolException ex) {
080        throw new InvalidObjectException("Couldn't resolve symbol:" + syms);
081      }
082    }
083  }
084}