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.seq.io;
024
025import org.biojava.bio.symbol.IllegalSymbolException;
026import org.biojava.bio.symbol.IntegerAlphabet;
027import org.biojava.bio.symbol.Symbol;
028
029/**
030 * @author Mark Schreiber
031 */
032public class SubIntegerTokenization extends WordTokenization {
033    public SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet alpha) {
034        super(alpha);
035    }
036
037    public Symbol parseToken(String seq)
038        throws IllegalSymbolException
039    {
040        try {
041            int i = Integer.parseInt(seq);
042            return ((IntegerAlphabet) getAlphabet()).getSymbol(i);
043        } catch (NumberFormatException ex) {
044            throw new IllegalSymbolException(ex, "Couldn't parse " + seq);
045        }
046    }
047
048    public String tokenizeSymbol(Symbol sym)
049        throws IllegalSymbolException
050    {
051        getAlphabet().validate(sym);
052        return sym.getName();
053    }
054}