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.dp.twohead;
023
024import org.biojava.bio.symbol.IllegalSymbolException;
025
026/**
027 * A cursor over a DP matrix.
028 *
029 * @author Matthew Pocock
030 */
031public interface PairDPCursor {
032  /** test wether the cursor can be advanced further */
033  boolean hasNext();
034  /** retrieve the next block of cells */
035  void next(Cell [][] cells) throws IllegalSymbolException;
036  /** press out a new correctly sized cell array */
037  Cell [][] press();
038  /** retrieve the depth of this cursor */
039  int [] getDepth();
040}