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.dp.onehead;
024
025import org.biojava.bio.symbol.Symbol;
026import org.biojava.bio.symbol.SymbolList;
027
028/**
029 * Encapsulates the dynamic programmming matrix, and the context within algorithms work.
030 * The cursor should put DP.MAGICAL_SYMBOL symbols at either end of the sequence.
031 *
032 * @author Matthew Pocock
033 */
034public interface DPCursor {
035  /**
036   * The symbol list being looped over.
037   */
038  SymbolList symList();
039  
040  /**
041   * <p>
042   * The length of the sequence.
043   * </p>
044   *
045   * <p>
046   * The matrix may allocate length+1 columns.
047   * </p>
048   */
049  int length();
050  
051  /**
052   * The current column of the matrix.
053   */
054  double [] currentCol();
055  
056  /**
057   * The previous column.
058   */
059  double [] lastCol();
060  
061  /**
062   * The current symbol.
063   */
064  Symbol currentRes();
065  
066  /**
067   * The previous symbol.
068   */
069  Symbol lastRes();
070    
071  /**
072   * Can we advance?
073   */
074  boolean canAdvance();
075  
076  /**
077   * Advance.
078   */
079  void advance();
080}