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 */
021package org.biojava.bio.seq.io;
022
023import java.io.IOException;
024
025import org.biojava.bio.symbol.Alphabet;
026import org.biojava.bio.symbol.IllegalSymbolException;
027import org.biojava.bio.symbol.Symbol;
028
029/**
030 * Encapsulate a stream of Symbols being parsed from some input
031 * stream.  This allows SymbolList creation to be fully decoupled from
032 * stream parsing.
033 *
034 * @author Thomas Down
035 * @since 1.1 [newio proposal]
036 */
037
038public interface SymbolReader {
039    /**
040     * Find the alphabet of all symbols which may be returned by
041     * this SymbolReader.  <strong>NOTE:</strong> SymbolList
042     * implementations are expected to perform any necessary
043     * validation of returned Symbols.  Client code should
044     * not need to perform any extra validation.
045     */
046
047    public Alphabet getAlphabet();
048
049    /**
050     * Return a single symbol from the stream.
051     *
052     * @throws IOException if an error occured on the stream, or the
053     *                     end of the stream has already been reached.
054     * @throws IllegalSymbolException if a parse error occured.
055     */
056
057    public Symbol readSymbol() throws IOException, IllegalSymbolException;
058
059    /**
060     * Read one or more symbols from the stream.
061     *
062     * @param buffer the destination for read symbols.
063     * @param start a start offset within the buffer.
064     * @param length the maximum number of Symbols to read.
065     *
066     * @return the number of Symbols which were actually read.
067     *
068     * @throws IOException if an error occured on the stream, or the
069     *                     end of the stream has already been reached.
070     * @throws IllegalSymbolException if a parse error occured.
071     */
072
073    public int readSymbols(Symbol[] buffer,
074                           int start,
075                           int length)
076            throws IOException, IllegalSymbolException;
077
078    /**
079     * Determine if there are more symbols left to read in this stream.
080     */
081
082    public boolean hasMoreSymbols();
083}