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.twohead;
024
025import org.biojava.bio.dp.BackPointer;
026import org.biojava.bio.dp.IllegalTransitionException;
027import org.biojava.bio.dp.ScoreType;
028import org.biojava.bio.symbol.IllegalAlphabetException;
029import org.biojava.bio.symbol.IllegalSymbolException;
030
031/**
032 * @author Matthew Pocock
033 */
034public interface CellCalculatorFactory {
035  CellCalculator forwards(ScoreType scoreType)
036  throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException;
037
038  CellCalculator backwards(ScoreType scoreType)
039  throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException;
040
041  CellCalculator viterbi(ScoreType scoreType, BackPointer terminal)
042  throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException;
043}