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.biojavax;
023import org.biojava.bio.symbol.Alphabet;
024import org.biojava.bio.symbol.SymbolList;
025import org.biojavax.bio.BioEntry;
026
027/**
028 * This interface returns symbols or sequence for a given cross-reference.
029 * @author Richard Holland
030 * @author Mark Schreiber
031 * @since 1.5
032 */
033public interface CrossReferenceResolver {
034    
035    /**
036     * Given a cross reference, return the corresponding symbol list.
037     * @param cr the cross reference to look up.
038     * @param a the alphabet to construct the infinitely ambiguous symbol list
039     *        over if it cannot be found.
040     * @return the symbol list matching it. If none, return an
041     * infintely-ambiguous symbol list rather than null.
042     */
043    public SymbolList getRemoteSymbolList(CrossRef cr, Alphabet a);
044    
045    
046    /**
047     * Given the <code>CrossRef</code> return the corresponding
048     * <code>BioEntry</code>
049     * @param cr the cross reference
050     * @throws org.biojavax.CrossReferenceResolutionException if a problem occurs
051     *         during resolution.
052     * @return The cross referenced entry (most likely a <code>RichSequence</code>
053     *         or null if it cannot be found.
054     */
055    public BioEntry getRemoteBioEntry(CrossRef cr) 
056    throws CrossReferenceResolutionException;
057}