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;
023
024import org.biojava.bio.BioException;
025import org.biojava.bio.symbol.IllegalSymbolException;
026import org.biojava.bio.symbol.Symbol;
027
028/**
029 * interface implemented by objects that train HMMs.
030 *
031 * @author David Huen
032 */
033public interface HMMTrainer
034{
035    /**
036     * called to put the trainer into an initial state for a new
037     * round of training.
038     */
039    public void startCycle();
040
041    /**
042     * record that the specified symbol was emitted from the specified state.
043     */
044    public void recordEmittedSymbol(State state, Symbol symbol, double weight)
045        throws IllegalSymbolException;
046
047    /**
048     * record that a transition was observed between the specified states.
049     */
050    public void recordTransition(State source, State dest, double weight)
051        throws IllegalArgumentException;
052
053    /**
054     * indicate that a cycle of training is completed and the
055     * emission/transition matrices should be updated.
056     */
057    public void completeCycle()
058        throws BioException;
059}
060